Thermodynamics of Biochemical Reactions

Thermodynamics of Biochemical Reactions

Robert A. Alberty Massachusetts Institute of Technology Cambridge, MA

WILEYINTERSCIENCE A John Wiley and Sons Publication

Copyright

c'2003 by John Wiley & Sons, Inc. All rights reserved.

Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada.

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Library of Congress C a t a l o ~ i n ~ - i n - P u b l t i oData: n Alberty, Robert A. Thermodynamics of biochemical reactions / Robert A. Alberty. p. em. Includes bibliographical references and index. ISBN 0-471-22851-6 (cloth : acid-free paper) 1. Thermodynamics. 2. Physical biochemistry. 3. Bioenergetics. I. Title. QP517.T48 A42 2003 547'.2--d~21 2002155481 Printed in the United States of America 10987654321

Contents

vii

Preface

Chapter Chapter Chapter Chapter Chapter Chapter Chapter Chapter Chapter Chapter Chapter

1 Introduction to Apparent Equilibrium Constants 2 Structure of Thermodynamics 3 Chemical Equilibrium in Aqueous Solutions 4 Thermodynamics of Biochemical Reactions at Specified pH 5 Matrices in Chemical and Biochemical Thermodynamics

6 Systems of Biochemical Reactions 7 Thermodynamics of Binding of the Ligands by Proteins 8 Phase Equilibrium in Aqueous Systems 9 Oxidation-Reduction Reactions 10 Calorimetry of Biochemical Reactions 11 Use of Semigrand Partition Functions

1

19

35 57 89 105 121

141 153 171

179

Glossary

186

References

190

Part Two: Mathematica Solutions to Problems BasicBiochemData2.nb Solutions to Problems Index of Mathematica Programs Index

389

Preface

This book is about the thermodynamics of enzyme-catalyzed reactions that make up the metabolism of living organisms. It is not an introductory text, but the fundamental principles of thermodynamics are reviewed. The reader does need some background in thermodynamics, such as that provided by a first course in physical chemistry. The book uses a generalized approach to thermodynamics that makes it possible to calculate the effects of changing pH, free concenrations of metal ions that are bound by reactants, and steady-state concentrations of coenzymes. This approach can be extended to other types of work that may be involved in a living organism. The concepts involved in this approach are simple, but the equations become rather complicated. Biochemical reactions are written in terms of reactants like ATP that are made up of sums of species, and they are referred to as biochemical reactions to differentiate them from the underlying chemical reactions that are written in terms of species. The thermodynamics of biochemical reactions is independent of the properties of the enzymes that catalyze them. However, the fact that enzymes may couple reactions that might otherwise occur separately increases the number of constraints that have to be considered in thermodynamics. Biochemical thermodynamics is complicated for several reasons: (1) Biochemical reactants consist of sums of species whenever a reactant has a pK within about two units of the pH of interest or binds metal ions reversibly. (2) Species of a biochemical reactant are often ions, and the activity coefficients of ions are functions of ionic strength. (3) Enzyme catalysis may introduce constraints in biochemical reactions in addition to balances of atoms of elements. (4) Metabolism is sufficiently complicated that it is important to find ways to obtain a more global view. (5) In biochemistry other kinds of work, such as electric work, elongation work, and surface work may be involved. It is remarkable that the same basic reactions are found in all living systems. The most important thing about these reactions is that they provide the means to carry out the oxidation of organic matter in a sequence of steps that store energy that is needed for the synthesis of organic molecules, mechanical work, and other functions required for life. The theme of this book is that Legendre transforms make the application of thermodynamics more convenient for the users. The logic used here is a continuation of the process described by Gibbs that introduced the enthalpy H ,

...

V ~ U

Preface Helmholtz energy A, and the Gibbs energy G by use of Legendre transforms of the internal energy U . In Chapter 4 a Legendre transform is used to introduce pH and pMg as independent intensive variables. In Chapter 6 the steady-state concentrations of various coenzymes are introduced as independent intensive variables in discussing systems of enzyme-catalyzed reactions. In Chapter 8 a Legendre transform is used to introduce the electric potential of a phase as an independent intensive variable. These uses of Legendre transforms illustrate the comment by Callen (1985)that "The choice of variables in terms of which a given problem is formulated, while a seemingly innocuous step, is often the most crucial step in the solution." Choices of dependent and independent variables are not unique, and so choices can be made to suit the convenience of the experimenter. Gibbs has provided a mathematical structure for thermodynamics that is expandable in many directions and is rich in interrelationships between measurable properties because thermodynamic properties obey all the rules of calculus. This book on thermodynamics differs from others in its emphasis on the fundamental equations of thermodynamics and the application of these equations to systems of biochemical reactions. The emphasis on fundamental equations leads to new thermodynamic potentials that provide criteria for spontaneous change and equilibrium under the conditions in a living cell. The equilibrium composition of a reaction system involving one or more enzyme-catalyzed reactions usually depends on the pH, and so the Gibbs energy G does not provide the criterion for spontaneous change and equilibrium. It is necessary to use a Legendre transform to define a transformed Gibbs energy G' that provides the criterion for spontaneous change and equilibrium at the specified pH. This process brings in a transformed entropy S' and a transformed enthalpy H ' , but this new world of thermodynamics is similar to the familiar world of G, S , and H , in spite of the fact that there are significant differences. Since coenzymes, and perhaps other reactants, are in steady states in living cells, it is of interest to use a Legendre transform to define a further transformed Gibbs energy G" that provides the criterion for spontaneous change and equilibrium at a specified pH and specified concentrations of coenzymes. This process brings in a further transformed entropy S" and a further transformed enthalpy H", but the relations between these properties have the familiar form. Quantitative calculations on systems of biochemical reactions are sufficiently complicated that it is necessary to use a personal computer with a mathematical application. Mathematica'~'"(Wolfram Research, Inc. 100 World Trade Center, Champaign, IL, 61820-7237)is well suited for these purposes and is used in this book to make calculations, construct tables and figures, and solve problems. The last third of the book provides a computer-readable database, programs, and worked-out solutions to computer problems. The database BasicBiochemData2 is available on the Web at http:,'/www.mathsource.com/cgi-bin/msitem?O211-662. Systems of biochemical reactions can be represented by stoichiometric number matrices and conservation matrices, which contain the same information and can be interconverted by use of linear algebra. Both are needed. The advantage of writing computer programs in terms of matrices is that they can then be used with larger systems without change. This field owes a tremendous debt to the experimentalists who have measured apparent equilibrium constants and heats of enzyme-catalyzed reactions and to those who have made previous thermodynamic tables that contain information needed in biochemical thermodynamics. Although I have been involved with the thermodynamics of biochemical reactions since 1950, I did not understand the usefulness of Legendre transforms until 1 had spent the decade of the 1980s working on the thermodynamics of petroleum processing. During this period I learned from Irwin Oppenheim (MIT) and Fred Krambeck (Mobil Research and Development) about Legendre transforms, calculations using matrices, and semigrand partition functions. In the 1990s 1 returned to biochemical thermodynamics and profited from many helpful

Preface discussions with Robert N. Goldberg (NIST). The new nomenclature that is used here was recommended by an IUPAC-IUBMB report by Alberty, CornishBowden, Gibson, Goldberg, Hammes, Jencks, Tipton, and Veech in 1994. The use of Legendre transforms in chemical thermodynamics is the subject of an IUPAC Technical Report by Alberty, Barthel, Cohen, Ewing, Goldberg, and Wilhelm (2001). I am indebted to NIH for award 5-R01-GM48458 for support of my research on biochemical thermodynamics. My Associate Managing Editor, Kristin Cooke Fasano of John Wiley and Sons, was very helpful. Robert A. Alberty Cambridge, Massachusetts

ix

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty Copyright 0 2003 John Wiley & Sons, Inc. ISBN 0-471-22851-6

1.6

Brief History of the Thermodynamics of Biochemical Reactions Acid Dissociation Constants and Dissociation Constants of Complex Ions Binding of Hydrogen Ions and Magnesium Ions by Adenosine Triphosphate Apparent Equilibrium Constants of Biochemical Reactions Production of Hydrogen Ions and Magnesium Ions in the Hydrolysis of Adenosine Triphosphate pKs of Weak Acids

Two types of equilibrium constant expressions are needed in biochemistry. The thermodynamics of biochemical reactions can be discussed in terms of species like ATP4-, HATP3-, and MgATP2- or in terms of reactants (sums of species) like ATP. The use of species corresponds with writing chemical reactions that balance atoms of elements and electric charges; the corresponding equilibrium constants are represented by K . This approach is required when chemical details are being discussed, as in considering the mechanism of enzymatic catalysis. But discussion in terms of metabolism must involve, in great deal detail, acid dissociation constants and dissociation constants of complexes with metal ions. Therefore metabolism is discussed by writing biochemical reactions in terms of reactants that is, sums of species, like ATP-at a specified pH and perhaps specified concentrations of free metal ions that are bound reversibly by reactants. Biochemical reactions d o not balance hydrogen ions because the pH is held constant, and they do not balance metal ions for which free concentrations are held constant. When the pH is held constant, there is the implication that acid or alkali will be added to the system to hold the pH constant if the reaction produces or consumes hydrogen ions. In actual practice a buffer is used to hold the pH nearly constant, and the pH is measured at equilibrium. The corresponding equilibrium constants are represented by K ' , which are referred to as apparent equilibrium constants because they are functions of pH and perhaps the free concentrations

1

2

Introduction to Apparent Equilibrium Constants of one or more free metal ions. Biochemical thermodynamics is more complicated than the chemical thermodynamics of reactions in aqueous solutions because there are more independent variables that have t o be specified. This introductory chapter is primarily concerned with the hydrolysis of ATP at specified 7; P , pH, pMg, and ionic strength. The thermodynamics of the hydrolysis of ATP and closely related reactions have received a good deal of attention because of the importance of these reactions in energy metabolism.

1.1 BRIEF HISTORY OF THE THERMODYNAMICS OF BIOCHEMICAL REACTIONS The first major publication on the thermodynamics of biochemical reactions was by Burton in Krebs and Kornberg, Energy Transformations in Living Matter, 1957. Before that time, apparent equilibrium constants had been measured for a number of enzyme-catalyzed reactions, but Burton recognized that these apparent equilibrium constants together with standard Gibbs energies of formation A,Go of species determined by chemical methods can yield Af Go for biochemical species to make a table that can be used to calculate equilibrium constants of biochemical reactions that have not been studied (Burton and Krebs, 1953). In retrospect it is easy to see that in 1953 to 1957 there were some problems that were apparently not clearly recognized or solved. Since Burton was the first, it is worth saying a little more about his 1957 thermodynamic tables. The first table gives Af Go values for about 100 species in biochemical reactions. A large number of these values were taken from chemical thermodynamic tables available in the 1950s, but a number were new values calculated from measured apparent equilibrium constants for enzyme-catalyzed reactions. Af Go values of species can be readily calculated when the reactants in the enzyme-catalyzed reaction are all single species and AfGo values are known for all of the reactants except one. It is noteworthy that Burton omitted the species of orthophosphate from his table and that he was not able to include species of ATP, ADP, NAD,,, and NAD,,,. His second table gives standard Gibbs energy changes at pH 7 for oxidation-reduction reactions that were calculated using the convention that [H'] = 1 mol L-' at pH 7; the symbol AC' was used for this quantity. This table also gives the corresponding standard cell potentials for these reactions. The third table gives AG' values at pH 7 for a number of reactions in glycolysis and alcoholic fermentation. The fourth table is on the citric acid cycle, and the fifth table is on Gibbs energies of hydrolysis. When a biochemical reaction is studied at a pH where there is a predominant chemical reaction, it is possible to discuss thermodynamics in terms of species. But when some reactants are represented by an equilibrium distribution of several species with different numbers of hydrogen atoms, this approach is not satisfactory. The quantitative treatment of reactions involving reactants with pKs in the neighborhood of pH 7 was not possible until acid dissociation constants of these reactants had been determined. Some measurements of acid dissociation constants of ATP and related substances (Alberty, Smith, and Bock, 1951) and dissociation constants of ionic complexes of these substances with divalent cations (Smith and Alberty, 1956) were made in this period. In the 1960s there was a good deal of interest in the thermodynamics of the hydrolysis of ATP and of other organic phosphates (Alberty, 1968, 1969; Phillips, George, and Rutman, 1969), but standard Gibbs energies of species were not calculated. The measurement of apparent equilibrium constants for biochemical reactions was extended in the 1970s (Guynn and Veech, 1973; Veech et al., 1979) and 1980s (Tewari and Goldberg, 1988). In 1969 Wilhoit picked up where Burton had left off and compiled the standard thermodynamic properties A,Go and A,Ho of species involved in biochemical reactions. He recognized the problems involved in including species

1.2 Acid Dissociation Constants and Dissociation Constants of Complex Ions of ATP in such a table and made a suggestion as to how to handle it. In 1977 Thauer, Jungermann, and Decker published a table of standard Gibbs energies of formation of many species of biochemical interest, and showed how to adjust standard Gibbs energies of reaction to pH 7 by adding mAfGo(H+),where m is the net number of protons in the reaction. During the 1960s and 1970s, new nomenclature for treating the thermodynamics of biochemical reactions was developed, including the use of K ' for the apparent equilibrium constant written in terms of sums of species, but omitting [H']. These changes led to the publication of Recommendations ,for Measurement and Presentation of Biochemical Equilibrium Data by an IUPACIUB Committee (Wadso, Gutfreund, Privalov, Edsall, Jencks, Armstrong, and Biltonen, 1976). Goldberg and Tewari published an evaluation of thermodynamic and transport properties of carbohydrates and their monophosphates in 1989 and of the ATP series in 1991. Miller and Smith-Magowan published on the thermodynamics of the Krebs cycle and related compounds in 1990. Alberty (1992a, b) pointed out that when the pH or the free concentration of a metal ion is specified, the Gibbs energy C does not provide the criterion for spontaneous change and equilibrium. When intensive variables in addition to the temperature and pressure are held constant, it is necessary to define a transformed Gibbs energy G ' by use of a Legendre transform, as discussed in Chapters 2 and 4. This leads to a complete set of transformed thermodynamic properties at specified pH, that is, a transformed entropy S', transformed enthalpy H ' , and a transformed heat capacity at constant pressure Cim. These changes led to the publication of Recommendations for Nonienclature and Tables in Biochemical Thermodynamics by an IUPAC-IUBMB Committee (Alberty, Cornish-Bowden, Gibson, Goldberg, Hammes, Jencks, Tipton, Veech, Westerhoff, and Webb, 1994). This introductory chapter describes the thermodynamics of biochemical reactions in terms of equilibrium constants and apparent equilibrium constants and avoids references to other thermodynamic properties, which are introduced later.

W

1.2 ACID DISSOCIATION CONSTANTS AND DISSOCIATION CONSTANTS OF COMPLEX IONS

Strictly speaking, equilibrium constant expressions for chemical reactions involving ions in aqueous solutions should be written in terms of activities a, of species, rather than concentrations. The activity of species i is given by ai = yici, where y i is the activity coefficient, which is a function of ionic strength. Activity coefficients of neutral molecules are close to unity in dilute aqueous solutions, but the activity coefficients of ions may deviate significantly from unity, depending on their electric charges and the ionic strength. The ionic strength of a solution is defined by I = ($zzci, where zi is the charge on ion i and c, is its concentration on the molar scale. When dilute aqueous solutions are studied, the ionic strength is under the control of the investigator and is essentially constant when the composition changes during a reaction. Thus it is convenient to take equilibrium constants and other thermodynamic properties to be functions of the ionic strength so that equilibrium constant expressions can be written in terms of concentrations. The exception to this statement is H,O. In dilute aqueous solutions the convention in thermodynamics is to omit [HzO] in the expression for the equilibrium constant because its activity remains essentially at unity. In 1923 Debye and Hckel showed that the activity coefficient yi of an ion decreases with increasing ionic strength, according to logyi = - A z , 2I 1 / 2 where A

= 0.510651 L-'"

(1.2-1)

mol'i2 at 298.15 K in water at a pressure of 1 bar. This

3

4

Introduction to Apparent Equilibrium Constants is referred to as a limiting law because it becomes more accurate as the ionic strength approaches zero. At ionic strengths in the physiological range, 0.05 to 0.25 M, there are significant deviations from equation 1.2-1. Of the several ways to extend this equation empirically to provide approximate activity coefficients in the physiological range, the most widely used equation is (1.2-2) This is referred to as the extended Debye-Hiickel equation. It is an approximation that gives a good fit of data at low ionic strengths (Goldberg and Tewari, 1991) when B = 1.6 L”’ mol-’’’. Better fits can be obtained with more complicated equations with more parameters, but these parameters are not known for solutions involved in studying biochemical reactions. The way that thermodynamic properties vary with the ionic strength is discussed in more detail in Section 3.6. Since hydrogen ions and metal ions, like Mg”, are often reactants, it IS convenient to define the pH, as -log[H+], where c refers to concentrations. and pMg as -log[Mg2+]. However, a glass electrode measures pH, = - log{y(H+)[H+]} where a refers to activity. Thus PH,

=

-log{-?(H+)j

+ PH,

(1.2-3)

Substituting the extended Debye-Hckel equation in this equation yields (Alberty, 2001d) PH,

-

PH,

=

AI”~ 1 1.61’12

+

(1.2-4)

The differences between the measured pH, and the pH, used in biochemical thermodynamics are given as a function of ionic strength and temperature in Table 1.1. These are the adjustments to be subtracted from pH, obtained with a pH meter to obtain pH,, which is used in the equations in this book. pH, is lower than pH, because the ion atmosphere of H + reduces its activity. In the rest of the book, the subscript “c” on pH will be omitted so that pH = -log[H+]. In considering reactions in biochemical systems it is convenient to move the activity coefficients into the equilibrium constants. For example, the equilibrium constant expression for the dissociation of a weak acid can be written as follows: HA

=

H+ +A-

(1.2-5)

(1.2-6)

The acid dissociation constant K , is independent of ionic strength, but the acid dissociation constant K , depends on the ionic strength, as indicated by equation 1.2-7. The equilibrium constant expression in equation 1.2-7 will be used in the rest of the book, but the subscript “c” will be omitted. This will make it possible for us to deal with concentrations of species, rather than activities. The same considerations apply to the dissociations of complex ions. For example, the equilibrium expression for the dissociation of a complex ion with a magnesium ion can be written as follows: MgA’

=

Mg2+ + A-

(1.2-8) (1.2-9)

1.3 Binding of Hydrogen Ions and Magnesium Ions by Adenosine Triphosphate Table 1.1 pH,-pH, as a Function of Ionic Strength and Temperature IIM

10°C

25°C

40°C

0 0.05 0.1 0.15 0.2 0.25

0 0.082 0.105 0.119 0.130 0.138

0 0.084 0.107 0.122 0.133 0.142

0 0.086 0.110 0.125 0.137 0.146

Source: R. A. Alberty, J . Phys. Chenz. B 105, 7865 (2001). Copyright 2001 American Chemical Society.

where pMg = -log[Mg2+] and K,,, is a function of the ionic strength, as well as temperature. Strictly speaking, equations 1.2-7 and 1.2-9 should have co in the denominator, where cn = 1 M is the standard concentration, to make the equilibrium constant dimensionless (Mills et al., 1993). However, the co is omitted in this book in order to simplify expressions for equilibrium constants. Nevertheless, equilibrium constants are still considered to be dimensionless, so their logarithm can be taken. In using acid dissociation constants and the dissociation constants of complex ions, it is convenient to take the base 10 logarithms of equations 1.2-7 and 1.2-9 to obtain

(1.2-10) (1.2-11) where pK,, = -log KH, and pKMgA= -log KMgA are functions of ionic strength at constant temperature. Table 1.3 in the last section of this chapter gives the pKs of some weak acids of interest in biochemistry as a function of ionic strength. Note that the effect of ionic strength is larger for acids with larger charges. For polyprotic acids pK, applies to the weakest acid group, pK, to the second weakest, and so on, in the pH range considered (usually 5 to 9). The calculation of Table 1.3 is based on the extended Debye-Huckel equation.

W

1.3 BINDING OF HYDROGEN IONS AND MAGNESIUM IONS BY ADENOSINE TRIPHOSPHATE

Acid dissociation constants and dissociation constants of complex ions determine the concentrations of species that are present in a solution at equilibrium under specified conditions. Ionic dissociation reactions occur rapidly and tend to remain at equilibrium during an enzyme-catalyzed reaction. Since ATP (see Fig. 1.1) is the primary carrier of energy in biochemical systems and since a good deal is known about its binding properties, these properties are considered here in some detail. An ATP ion with four negative charges can bind five hydrogen ions in strongly acidic solutions, but biochemistry is primarily concerned with the neutral region. We will consider only the hydrogen ion bindings that affect equilibrium in this region, namely the terminal phosphate group with a pK about 7 and the

5

6

Introduction to Apparent Equilibrium Constants

Adenine

D -Ribose

OH

OH

Adenosine Adenosine inonophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate ( A n )

Figure 1.1 Structure of adenosine triphosphate

adenine group with pK about 4. The other three pKs are in the neighborhood of 2 or below and can be ignored in treating biochemical reactions. The anions of ATP bind metal ions as well as hydrogen ions. The dissociation constants for the complex ions that are formed can be determined by use of acid titrations because the binding of a metal ion reduces the apparent pK for the phosphate group (Alberty, Smith, and Bock, 1951; Smith and Alberty, 1956; Silbey and Alberty, 2001). The apparent pK of the phosphate group is the midpoint of the titration of H,POi- in the presence of magnesium ions at the desired concentration of free metal ions. Because of the importance of ATP in energy metabolism, a great deal of data on the acid dissociation constants and the dissociation constants of complex ions of ATP, ADP, AMP, and Pi are available. Goldberg and Tewari (1991) and Larson, Tewari, and Goldberg (1993) critically evaluated these data including that on glucose 6-phosphate (G6P). The values for acid dissociation constants and magnesium complex ion dissociation constants involved in the ATP series are given in Table 1.2. Since ATP is made up of three species in the physiological pH range in the absence of metal ions that are bound, its concentration is given by [ATP]

=

[ATP4-]

+ [HATP3-] + [H,ATP2-]

(1.3-1)

Substituting the expressions for the two acid dissociation constants yields [ATP]

=

[ATP4-]

(1.3-2) KIATPK2ATP

The mole fraction r of the ATP in the ATP4- form at a specified concentration of hydrogen ions is given by 1

r(ATPP4) = 1+-

CH'1 KIATP

W+I2

+

(1.3-3)

KlATPK2ATP

The mole fractions of ATP in the other two forms are readily derived: CH'I r(HATP3 -)

KIATP

=

1

CH' I I1

CH'I'

(1.3-4)

1.3 Binding of Hydrogen Ions and Magnesium Ions by Adenosine Triphosphate Table 1.2

Equilibrium Constants in the ATP Series at 298.15 K

Reaction

pK(I=0) ~-

~

K(I=0)

~

H A M P - = H + + AMP26.73 H2AMP = H + + HAMP3.99 MgAMP = Mg2+ + AMP2 2.79 HADP2- = H + + ADP-3 KI,,, 7.18 H2ADP~- = H + HADP' K2ADP 4'36 MgADP- = Mg2+ + ADP3K3,DP 4.65 MgHADP = Mg2' + HADP2- K,,,, 2.50 HATP3- = H + + ATP4KiATP 7.60 H , A T P ~ -= H + + HATP" K,,,, 4.68 MgATP2- = Mg2+ + ATP4KMTP 6.18 MgHATP- = Mg2+ + HATP3 K,,, 3.63 Mg2ATP = Mg2+ + MgATP2- K,,,, 2.69 H,PO, = H + + HP0:7.22 MgHPO, = Mg2+ + HPO;2.71 HG6P- = H + + G6P26.42 MgG6P = Mgzi + G6P22.60 Hadenosine' = H + + adenosine 3.50 ATP4- + H,O = ADP3- + HP0:- + H + ADP3--+ H,O = AMP2- + HP0;- + H + AMP2- + H,O = adenosine + HP0;G6P2- + H,O = glucose + HP0;ATP4- + glucose = ADP3- + G6P2- + H + 2ADP3 = ATP4 + AMP2 +

K(I=0.25 M) ~~

1.862 x 1.023 x 1.622 x 6.607 x lo-' 4.365 x 1 0 - j 2.239 x 10-5 3.162 x 2.512 x lo-* 2.089 x 10-5 6.607 x 2.344 x 2.042 x 6.026 x lo-' 1.950 x 3.802 x 2.512 x 3.162 x 2.946 x lo-' 6.622 x lo-' 1.894 x 10' 8.023 x 10' 3.671 x 2.248 x lo-'

~~

6.877 x 1.966 x 2.212 x lo-, 4.689 x 1.612 x 1.128 x 4.313 x 3.426 x 1.483 x 1.229 x lo-, 1.181 x 2.785 x 1 -' 2.225 x lo-' 2.66 x 1.404 x 3.462 x lo-' 3.162 x

Source: R. A. Alberty and R. N. Goldberg, Biochem., 31, 10612 (1992). Copyright 1992 American Chemical Society.

r(H2ATP2-) =

KIATI'KZATP

(1.3-5) KZATP

These mole fractions are plotted versus pH at 298.15 K and I = 0.25 M in Fig. 1.2. Since it is possible to calculate the mole fractions of the various species of ATP at a specified pH, the average binding of hydrogen ions RHcan be calculated by use of

NH =

O[ATP4-]

+ 1[HATP3-] + 2[H,ATP2-] [ATPI

(1.3-6)

rr

I t

_- -_--

Figure 1.2 Mole fractions of three species of ATP plotted versus pH at 298.15K and I = 0.25 M (see Problem 1.1).

7

8

Introduction to Apparent Equilibrium Constants The numbers of hydrogen ions bound that are calculated using this equation are based on the arbitrary convention of not counting the additional 12 hydrogen atoms in ATP. Thus, the average number RE,of hydrogen ions bound by ATP is given by

CH'1

2CH'I2

,

(1.3-7)

At very high pH, the binding of H + approaches zero, and below pH 4 it approaches 2. In dealing with binding, it is convenient to use the concept of a binding polynomial (Wyman 1948, 1964, 1965, 1975; Edsall and Wyman, 1958; Hermans and Scheraga, 1961; Schellman, 1975, 1976; Wyman and Gill, 1990). The polynomial in the denominator of equation 1.3-7 is referred to as the binding polynomial P. It is actually a kind of partition function because it gives the partition of a reactant between the various species that make it up. The binding polynomial for the binding of hydrogen ions by ATP is given by (1.3-8)

The average binding of hydrogen ions is given by N- w - [H'] P

d l_ nP d P - d l n P - _-1_ _ dLH'] - dln[H+] ln(10) dpH

(1.3-9)

Equation 1.3-7 is readily obtained from equation 1.3-8 by use of equation 1.3-9. Substituting the values of the two acid dissociation constants of ATP at 298.15 K, 1 bar, and I = 0.25M from Table 1.2 into equation 1.3-7 or 1.3-9 yields the plot of Nt, versus pH that is shown in Fig. 1.3. Figure 1.3 shows that the acid titration curve for a weak acid can be calculated from its pKs, and this raises the question as to how the pKs can be calculated from the titration curve. This can be done by first integrating equation 1.3-9 to obtain the natural logarithm of the binding potential P: N H d[H'] JCH'I

=

i d l n P = In P + const.

(1.3-10)

or -ln(10)

I

. . .

N,pH

. .

4

. . . .

.

5

=

.

. .

d l n P = 1nP + const.

. . .

6

. .

.? 7

-.-.:-.

8

.

(1.3-1 1)

. .

9

pb,

Figure 1.3 Binding of hydrogen ions by ATP at 298.15K and I Problem 1.2).

= 0.25 M

(see

1.3 Binding of Hydrogen Ions and Magnesium Ions by Adenosine Triphosphate The acid dissociation constants can be calculated from In P by fitting the plot of P versus [H'] with a power series in [H']. ATP also binds magnesium ions as shown by the three complex ion dissociation constants in Table 1.2. Incorporating these species into equations 1.3-1 and 1.3-2 yields the following binding polynomial for ATP: P = l + - CH+I

+

+-CMg2+l

CH+I2 KIATPK2ATP

K3ATP

+

CMg2+ICH+I

CME2+I2

+

KlATPK4ATP

K3ATPK5ATP

(1.3-12) Now the binding of hydrogen ions is given by the following partial derivatives of the binding polynomial: -

N , = - [H'] P

(

dP d[H+]

) pMg

-1 (i31nP)pMg __ =[H'] ln(10) apH

--

(ainP) ~

pMg

(1.3-13) The average binding of magnesium ions NH is given by the following partial derivatives of the binding polynomial:

( 1.3-14)

These differentiations yield

N- ,

+ CMg2+ICH+I KlATPK2ATP

=

1

KlATPK4ATP

+( 1.3-15)

(1.3-16) Figure 1.4 shows a plot of NHversus pH at several values of pMg. It is evident that the apparent pK of ATP in the neighborhood of 7 is reduced to about 5 in

Figure 1.4 Binding of hydrogen ions by ATP at 298.15 K, I 5, and 6 (see Problem 1.3).

= 0.25 M,

and pMg 2, 3, 4,

9

10

Introduction to Apparent Equilibrium Constants

3

4

5

6

Figure 1.5 Binding of magnesium ions by ATP at 298.15 K. I 6, 7, 8, and 9 (see Problem 1.4).

7 = 0.25 M,

and pH 3, 4, 5,

a MgCl, solution with [Mg2+] = l o p 2 M at ionic strength 0.25 M. Experimental plots of this type make it possible to calculate K,,,, and K,,,, (Smith and Alberty, 1956). Figure 1.5 shows a plot of mMgversus pMg at several values of pH. As the hydrogen ion concentration is increased, the binding of magnesium ions is decreased because of the competition for the same sites. Equations 1.3-15 and 1.3-16 can be used to make three-dimensional plots of NMg and as functions of pH and pMg. These plots are given in Figs. 1.6 and 1.7. The back plane of Fig. 1.6 gives the hydrogen ion binding of ATP in the essential absence of Mg (more accurately, pMg > 6). At pMg 2 the apparent second pK of ATP is less than 5. Figure 1.7 shows that below pMg 5 there is essentially no binding of magnesium ion and that binding increases to a number a little greater than 1 at pMg 2 and pH > 6 but is eliminated by further reduction of the pH. Figures 1.4 to 1.7 can also be obtained by plotting derivatives of the binding potential (see equations 1.3-13 and 1.3-14), rather than by use of equations 1.3-15 and 1.3-16 (see Problems 1.5 and 1.6). A remarkable fact about Figs. 1.6 and 1.7 is that at any given pH and pMg. in Fig. 1.6, the slope in the pMg direction is the same as the slope in pH direction in Fig. 1.7 at that pH and pMg. This is because the mixed partial derivatives of

Figure 1.6 Plot of NH versus pH and pMg for ATP at 298.15 K and I Problem 1.5).

=

0.25 M (see

1.4 Apparent Equilibrium Constants of Biochemical Reactions

Figure 1.7 Plot of NMgversus pH and pMg at 298.15 K and I

=

0.25 M (see Problem 1.6).

a function like P are equal. ( 1.3-17)

In thermodynamics, this is referred to as a Maxwell equation. This equation is derived later in Section 4.8. Thus the effect of pMg on the binding of hydrogen ions is the same as the effect of pH on the binding of magnesium ions; in short, these are reciprocal effects. The bindings of these two ions are referred to as linked functions. Equation 1.3-17 can be confirmed by plotting these two derivatives, and the same plot is obtained in both cases. This would be a lot of work to do by hand, but since Mathematica' can take partial derivatives, this can be done readily with a computer. The two plots are identical and are given in Fig. 1.8.

1.4 APPARENT EQUILIBRIUM CONSTANTS OF BIOCHEMICAL REACTIONS In this section we consider the hydrolysis of adenosine triphosphate to adenosine diphosphate and inorganic phosphate, first at a specified pH in the absence of metal ions that are bound and then in the presence of magnesium ions. At

Figure 1.8 Plot of (aN,,/apH) I = 0.25 M (see Problem 1.6).

or (am,/apMg) versus pH and pMg at 298.15K and

11

12

Introduction to Apparent Equilibrium Constants specified pH (and pMg) the biochemical reaction is written in terms of sums of species: ATP

+ H 2 0 = ADP + PI

(1.4-1)

Biochemical textbooks often add a H + on the right-hand side, but this is stoichiometrically incorrect when the pH is held constant, as we will see in the next section. It is also wrong, in principle, as we will see in Chapter 4, since hydrogen atoms are not balanced by biochemical reactions because the pH is held constant. The statement that the pH is constant means that in principle acid or alkali is added to the reaction system as the reaction occurs to hold the pH constant. In practice, a buffer is used to hold the pH nearly constant. and the pH is measured at equilibrium. The expression for the apparent equilibrium constant K ' for reaction 1.4-1 is (1.4-2) because the activity of water is taken as unity in dilute aqueous solutions at each temperature. The apparent equilibrium constant K ' is a function of 7; P, pH. pMg, and ionic strength. In the neutral region in the absence of magnesium ions, ATP, ADP, and Pi each consist of two species, and so K'

=

([ADP3-]

+ [HADP2-])([HPO~-] + [H2P0,]) [ATP4-] + [HATP3-]

[ADP3-l[HPoi-I( l + [ H + l / K I A D P ) ( l

--

[ATP4-]

(1

f [H+I/KIPi)

+ ~H+I/K,ATP) (1.4-3)

where Krefis the chemical equilibrium constant for the chemical reference reaction ATP4-

+ H,O

Kref

=

= ADP3-

+ HPOi- + H +

[ADP3-][HPOi-] [H '1 [ATP4-]

(1.4-4) (1.4-5)

Since the acid dissociation constants are known, the value of Kref can be calculated from the value of K ' at a pH in the neutral region in the absence of metal ions by using equation 1.4-3. Values of Krefat zero ionic strength are given in Table 1.2 for six reference reactions. When magnesium ions or other metal ions are bound reversibly and a wider range of pH is considered, equation 1.4-3 becomes more complicated. Therefore it is convenient to use the nomenclature of binding polynomials introduced in equation 1.3-8. The binding polynomial of ATP is given in equation 1.3-12, and the binding potentials for ADP and PI are as follows: PAD,

=

1

+ CH'1

W+I2

+

~

KIADP

KlADPK2ADP

(1.4-7) Thus the apparent equilibrium constant for the hydrolysis of ATP as a function of [H'] and [Mg2+] is given by

K'

= KrefPADPPPj

(1.4-8)

W+lPATP

Since the chemical equilibrium constants in this equation are known at zero ionic strength at 298.15 K and are given in Table 1.2, K' can be calculated at any pH

1.5 Production of Hydrogen Ions and Magnesium Ions

Figure 1.9 Plot of the base 10 logarithm of the apparent equilibrium constant for the hydrolysis of ATP to ADP and Pi at 298.15 K and 0.25 M ionic strength (see Problem 1.7).

in the range 3 to 9 and any pMg in the range 2 to 7 at a specified ionic strength. The dependence of K ' on pH and pMg is shown in Fig. 1.9; log K ' is plotted versus pH and pMg since K' varies over many powers of ten in these ranges of pH and pMg. In Chapter 4 we will be interested in -RTln K ' , where the gas constant R is 8.31451 J K - l mol-', and so this quantity in kJ mol-I is plotted versus pH and pMg in Fig. 1.10. The pH dependencies of the apparent equilibrium constants of biochemical reactions were discussed by Alberty and Cornish-Bowden in 1993.

1.5 PRODUCTION OF HYDROGEN IONS AND MAGNESIUM IONS IN THE HYDROLYSIS OF ADENOSINE TRIPHOSPHATE The calculation of the binding of hydrogen ions N, for ATP discussed in Section 1.3 can be applied to ADP and Pi so that the change in binding of H + in the hydrolysis of ATP can be calculated using ArNH= &J,(ADP)

+ NH(Pi)- N,(ATP)

-

1

(1.5-1)

where the - 1 is for the two protons in water minus the proton in HPO,, which is treated as the base species of inorganic phosphate in the reference reaction. The

Figure 1.10 Plot of - R T l n K ' in kJ mol-' versus pH at 298.15K and 0.25M ionic strength (see Problem 1.7).

13

14

Introduction to Apparent Equilibrium Constants change in the binding of magnesium ions in the hydrolysis of ATP at specified pH is given by ( 1.5-2)

Since N H and NMgcan be calculated for these reactants, Ar N, and ArNMgcan be calculated as a function of pH and pMg. However, when a computer is available there is an easier way to d o this by using equation 1.3-13 for the binding of hydrogen ions and 1.3-14 for the binding of magnesium ions. For example, equation 1.5-1 can be written

(1.5-3) where of course T and P are also held constant. Note that this same result is obtained by simply differentiating the expression for In K ' (equation 1.4-8) with respect to pH. Thus (1.5-4) The change in binding of Mg2+ ions can be calculated using

(1.5-5) Since K ' is a pretty complicated function of pH and pMg, it would be very difficult to carry these calculations out by hand. However, with Mathernatica the calculations can be done quickly. Figure 1.11 shows the change in the binding of hydrogen ions in the hydrolysis of ATP as a function of pH and pMg. At high pH the change in binding is -1 mole of H + per mole of ATP hydrolyzed, as expected from the reference reaction, which predominates at high pH. The products bind fewer hydrogen ions, and so there is a net production of hydrogen ions in the biochemical reaction. In the presence of magnesium ions there are conditions where the change in binding is positive, which indicates that hydrogen ions are consumed in the hydrolysis of ATP under these conditions. Figure 1.12 shows the change in binding of magnesium ions as a function of pH and pMg. Magnesium ions are always produced in the hydrolysis because

Figure 1.11 Change in the binding of hydrogen ions in the hydrolysis of ATP as a function of pH and pMg at 298.1SK and 0.25 M ionic strength (see Problem 1.8).

1.6 pKs of Weak Acids

Figure 1.12 Change in the binding of magnesium ions in the hydrolysis of ATP at 298.1 5 K and 0.25 M ionic strength (see Problem 1.9).

they are more strongly bound by ATP than by ADP and Pi. The change in binding approaches zero as the concentration of free magnesium ions approaches zero, and it also approaches zero at high concentrations of magnesium ion and high pH, where the principal reaction is Mg,ATP H,O = MgADPMgHPO, H’. Figures 1.11 and 1.12 are related in the same way as the binding curves for a single reactant (see equation 1.3-15); that is, the slope of the plot of ArNHin the pMg direction is the same as the slope of the plot of ArNMg in the pH direction. This is a consequence of the reciprocity relation:

+

+

+

(1.5-6) This equation is derived later in Section 4.8. The change in the value of the apparent equilibrium constant with pH and pMg and the production or consumption of hydrogen ions and magnesium ions by the biochemical reaction are really two sides of the same coin. The effects of pH and pMg on K’ are due to the fact that the biochemical reaction produces or consumes these ions. This is an example of Le Chatelier’s principle, which states that when an independent variable of a system at equilibrium is changed, the equilibrium shifts in the direction that tends to reduce the effect of the change. If the reaction produces hydrogen ions, lowering the pH will cause K ‘ to decrease because the system is doing what it can to reduce the effect of the pH change.

H

1.6 pKs OF WEAK ACIDS

In this chapter we have seen that acid dissociation constants are needed to calculate the dependence of apparent equilibrium constants on pH. In Chapter 3 we will discuss the calculation of the effects of ionic strength and temperature on acid dissociation constants. The database described later can be used to calculate pKs of reactants at 298.15 K at desired ionic strengths. Because of the importance of pKs of weak acids, Table 1.3 is provided here. More experimental measurements of acid dissociation constants and dissociation constants of complex ions with metal ions are needed because they are essential for the interpretation of experimental equilibrium constants and heats of reactions. A major database of acid dissociation constants and dissociation constants of metal ion complexes is provided by Martell, Smith, and Motekaitis (2001).

15

16

Introduction to Apparent Equilibrium Constants Table 1.3

pKs of Weak Acids at 298.15 K in Dilute Aqueous Solutions as a Function of Ionic Strength (See Problem 1.10)

Z=OM acetate acetylphosphate K acetylphosphate K , adenine ammonia ATP K , ATP K , ADP K , ADP K , AMP K , AMP K , adenosine bisphosphoglycerate citrate K , citrate K , isocitrate K , socitrate K , coenzyme A HCO, K , HZCO, K , cysteine dihydroxyacetone phosphate fructose 6-phosphate K fructose-l,6-biphosphate K , fructose-] ,6-biphosphate K , fumarate K fumarate K , galactose l-phosphate K glucose 6-phosphate K glutathione,,, glucose 1-phosphate K glyceraldehyde phosphate glycerol 3-phosphate malate K , oxalate K , phosphoenolpyruvate 2-phosphoglycerate 3-phosphoglycera te phosphate K , pyrophosphate K , pyrophosphate K , pyrophosphate K , ribose 1-phosphate K ribose 5-phosphate K , succinate K succinate K , succinylcoA thioredoxin,,, K thioredoxin,,, K ,

,

,

,

,

,

,

,

,

4.75 8.69 5.1 1 4.20 9.25 7.60 4.68 7.18 4.36 6.73 3.99 3.47 7.96 6.39 4.76 6.40 4.76 8.38 10.30 6.37 8.38 5.70 6.27 6.65 6.05 4.60 3.09 6.15 6.42 8.34 6.50 5.70 6.67 5.26 4.28 7.00 7.64 7.53 7.22 9.46 6.72 2.26 6.69 6.69 5.64 4.21 4.21 8.64 8.05

I

= 0.10 M

Z = 0.25 M

4.54 8.26 4.90 4.20 9.25 6.74 4.04 6.53 3.93 6.30 3.77 3.47 7.10 5.75 4.33 5.76 4.33 8.16 9.90 6.15 8.16 5.27 5.84 5.79 5.41 4.17 2.88 5.72 5.99 7.91 6.07 5.27 6.24 4.83 3.85 6.36 7.00 6.89 6.79 8.60 6.08 1.83 6.26 6.26 5.21 3.99 4.00 8.21 7.83

4.47 8.12 4.83 4.20 9.25 6.47 3.83 6.33 3.79 6.16 3.71 3.47 6.83 5.54 4.19 5.55 4.19 8.10 9.76 6.08 8.09 5.13 5.70 5.52 5.20 4.03 2.81 5.58 5.85 7.77 5.93 5.13 6.10 4.69 3.71 6.15 6.79 6.68 6.65 8.33 5.87 1.69 6.12 6.12 5.07 3.92 3.93 8.09 7.76

1.6 pKs of Weak Acids The equations and calculations described in this chapter are very useful, but so far we have not discussed thermodynamic properties other than equilibrium constants. The other properties introduced in the next three chapters provide a better understanding of the energetics and equilibria of reactions. We will consider the basic structure of thermodynamics in Chapter 2 and then to apply these ideas to chemical reactions in Chapter 3 and biochemical reactions in Chapter 4.

17

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty Copyright 0 2003 John Wiley & Sons, Inc. ISBN 0-471-22851-6

rn rn rn rn rn

2.1 2.2 2.3 2.4 2.5

rn 2.6 rn 2.7 rn 2.8

State of a System Fundamental Equation for the Internal Energy Maxwell Equations Gibbs-Duhem Equation and the Phase Rule Legendre Transforms for the Definition of Additional Thermodynamic Potentials Thermodynamic Potentials for a Single-Phase System with One Species Other Kinds of Work Calculation of Thermodynamic Properties of a Monatomic Ideal Gas from Derivatives of a Thermodynamic Potential

According to the first law of thermodinamics, there is a thermodynamic property U of a system, called the internal energy. The change in internal energy in a change in the state of a system is given by AU = q + w, where q is the heat flow into the system and w is the work done on the system. The work can be pressure-volume work, work of transport of electric charge, chemical work (more on this later), work of stretching an elastomer, and so on. The second law of thermodynamics has two parts. According to the first part there is a thermodynamic property S of a system, called the entropy. The change in entropy in a reversible change from one state of a system to another is given by AS = 417; where T is the absolute temperature. According to the second part of the second law, when a change takes place spontaneously in an isolated system, AS is greater than zero. This is a remarkable result because it provides a way to calculate whether a specified change in state can take place in a system on the basis of other types of measurements on the system. These conclusions apply to systems consisting of phases that are uniform in composition and do not have gradients of temperature or concentration in them. These two laws can be combined for a system involving only pressure-volume work to obtain dU = T d S - P d V This so-called fundamental equation shows two things: (1) thermodynamic properties of a system obey the rules of calculus and (2) the choice of independent variables (in this case S and V ) plays a very important role in thermodynamics. The second law can be used to show that when S and I/ are held constant, the internal energy U of a system must decrease

19

20

Chapter 2

Structure of Thermodynamics in a spontaneous process. For example, the internal energy of an isolated system decreases when a spontaneous process occurs in it because S and V are constant. If thermodynamics could not provide more than this, it would be difficult to use. Fortunately mathematics provides a way to introduce intensive variables as independent variables by using Legendre transforms. The concept of a Legendre transform is very important because it leads from the internal energy U to the enthalpy H and the Gibbs energy G; these thermodynamic properties are defined by H = U + PI/ and G = U + PV - TS = H - T S . In this book additional Legendre transforms are used to define the transformed Gibbs energy G' and the transformed enthalpy H ' at specified pH and pMg in Chapter 4 on biochemical reactions. In Chapter 6 further transformed Gibbs energies G" and further transformed enthalpies H " are introduced to discuss systems of biochemical reactions at specified concentrations of coenzymes. The construction of Legendre transforms is discussed in Section 2.5. It is also important to understand that all these properties obey all the rules of calculus. As a consequence these properties are related through fundamental equations, Maxwell equations, Gibbs-Helmholtz equations, and Gibbs-Duhem equations. The internal energy U , entropy, and the properties defined by Legendre transforms are referred to as thermodynamic potentials because, like the potential energy in mechanics, these extensive properties of a thermodynamic system give information about the direction of spontaneous change and the equilibrium state of the system. When work other than pressure-volume work is involved in a system, still more thermodynamic potentials can be defined by use of Legendre transforms, and these thermodynamic potentials provide criteria of equilibrium when sets of properties convenient for the experimenter are held constant. These various thermodynamic potentials are needed for the convenience of the experimenter. The thermodynamic potential used to provide a criterion of spontaneous change and equilibrium depends on the intensive variables that are held constant. Biochemical systems provide exceptional challenges to thermodynamics because the concentrations of hydrogen ions, certain metal ions, and coenzymes may be held constant, and electrical work, mechanical work, and surface work may be involved in addition to chemical work and PV work. When the equations in this chapter are applied to dilute electrolyte solutions, it is convenient to take the thermodynamic properties to be functions of the ionic strength. This is not treated in detail in this chapter, but is in the next chapter. This chapter deals with the thermodynamics of one-phase systems, and it is understood that the phase is homogeneous and at uniform temperature. The basic structure of thermodynamics provides the tools for the treatment of more complicated systems in later chapters. This book starts with the fundamentals of thermodynamics, but the reader really needs some prior experience with thermodynamics at the level of undergraduate thermodynamics (Silbey and Alberty, 2001). Legendre transforms play an important role in this chapter, and the best single reference on Legendre transforms is Callen (1960, 1985). Other useful references for basic thermodynamics are Tisza (1966), Beattie and Oppenheim (1979), Bailyn (1994), and Greiner, Neise, and Stocker (1995).

2.1 STATE OF A SYSTEM A system that is made up of a homogeneous mass of a substance at equilibrium can be described as being in a certain thermodynamic state that is characterized by certain properties. If forces of various types act on the system or more of the substance is added, the system is changed to a different state. It is remarkable that only a small number of properties have to be specified to completely characterize the equilibrium state of a macroscopic system. For a system containing a single substance, three properties suffice, if they are properly chosen. For example, the

2.2 Fundamental Equation for the Internal Energy state of a mass of an ideal gas is specified by its temperature 7; pressure P, and amount n because the volume V is given by V = nRT/P, where R is the gas constant. Alternatively, I! 7; P or I!P, n, or I! 7; n could be specified. An ideal gas is a special case, but three properties are sufficient to define the state of a simple system (that is one substance in one phase) provided one property is extensive. If work in addition to P V work is involved, more variables have to be specified. These properties and others that characterize the state of a system are referred to as state properties because they determine the state of the system. The internal energy U is also a state property. It is appropriate to call them state functions because they are independent of the path of change and can be manipulated by the operations of algebra and calculus. A thermodynamic property is said to be extensive if the magnitude of the property is doubled when the size of the system is doubled. Examples of extensive properties are volume V and amount of substance n. A thermodynamic property is said to be intensive if the magnitude of the property does not change when the size of the system is changed. Examples of intensive properties are temperature, pressure, and the mole fractions of species. The ratio of two extensive properties is an intensive property. For example, the ratio of the volume of a one-component system to its amount is the molar volume: V, = V/n. Experience shows that for a system that is a homogeneous mixture of N , substances, N , 2 properties have to be specified and at least one property must be extensive. For example, we can specify 7; P , and amounts of each of the N , substances or we can specify 7; P , and mole fractions x,of all but one substance, plus the total amount in the system. Sometimes we are only interested in the intensive state of a system, and that can be described by specifying N , 1 intensive properties for a one-phase system. For example, the intensive state of a solution involving two substances can be described by specifying 7; P, and the mole fraction of one of substances. When other kinds of work are involved, it is necessary to specify more variables, but the point is that when a small number of properties are specified, all the other properties of the system are fixed. This is in contrast with the very large number of properties that have to be specified to describe the microscopic state of a macroscopic system. In classical physics the complete description of a mole of an ideal gas would require the specification of 3 N , components in the three directions of spatial coordinates and 3 N , components of velocities of molecules, where N , is the Avogadro constant.

+

+

2.2 FUNDAMENTAL EQUATION FOR THE INTERNAL ENERGY The first and second laws of thermodynamics for a homogeneous closed system involving only P V work lead to the fundamental equation for the internal energy U: dU

=

TdS - P d V

(2.2-1)

where T is the temperature, S is the entropy of the system, P is the pressure, and V is the volume. The first law states that d U = dq - P d V when only pressurevolume work is involved and the second law states that d S > dq/z where q is heat and d indicates an inexact differential. The integral of an inexact differential depends on the path, but the integral of an exact differential does not. The test for exactness is given in Section 2.3. The greater than or equal sign indicates that the difl'erential entropy is equal to dq/T for a reversible process and is greater than dq/T in a spontaneous process. It is important to note that all five thermodynamic properties in equation 2.2-1 have exact differentials and that the fundamental equation for U is written in the notation of calculus. This means that these properties behave like mathematical functions so that further relations can be

21

22

Chapter 2 Structure of Thermodynamics obtained by use of the operations of calculus. The third law states that the entropy of each pure element or substance in a perfect crystalline form is zero at absolute zero. The entropy provides a criterion of spontaneous change and equilibrium at constant U and V because (dS),., 3 0. Thus the entropy of an isolated system can only increase and has its maximum value at equilibrium. The internal energy also provides a criterion for spontaneous change and equilibrium. That criterion is (dU),,, 6 0, which indicates that when spontaneous changes occur in a system described by equation 2.2-1 at constant S and V; U can only decrease and has its minimum value at equilibrium. The inequalities of the previous paragraph are extremely important, but they are of little direct use to experimenters because there is no convenient way to hold U and S constant except in isolated systems and adiabatic processes. In both of these inequalities, the independent variables (the properties that are held constant) are all extensive variables. There is just one way to define thermodynamic properties that provide criteria of spontaneous change and equilibrium when intensive variables are held constant, and that is by the use of Legendre transforms. That can be illustrated here with equation 2.2-1, but a more complete discussion of Legendre transforms is given in Section 2.5. Since laboratory experiments are usually carried out at constant pressure, rather than constant volume, a new thermodynamic potential, the enthalpy H, can be defined by H=U+PV

(2.2-2)

The differential of the enthalpy is given by dH

= dU

+ PdV+

VdP

(2.2-3)

Substituting equation 2.2-1 yields dH

=

TdS + VdP

(2.2-4)

The use of a Legendre transform has introduced an intensive property P as an independent variable. It can be shown that the criterion for spontaneous change and equilibrium is given by (dH),,, 3 0. The temperature can be introduced as an independent variable by defining the Gibbs energy G with the Legendre transform G=H-TS

(2.2-5)

The differential of the Gibbs energy is given by dG

= dH

-

TdS - S d T

(2.2-6)

Substituting equation 2.2-4 yields dG

= -SdT+

VdP

(2.2-7)

The use of this Legendre transform has introduced the intensive property T as an independent variable. It can be shown that the criterion for spontaneous change and equilibrium is given by (dG),,, 3 0. The Gibbs energy is so useful because T and P are convenient intensive variables to hold constant and because, as we will see shortly, if G can be determined as a function of T and P, then S, V, H, and U can all be calculated. Gibbs (1873) showed how to include the contributions of added matter to the fundamental equation by introducing the concept of the chemical potential p , of species i and writing the fundamental equation for the internal energy of a system involving P V work and changes in the amounts n, of species as v
represents the set of amounts of species, then 7; P, and { p i } can be determined by taking partial derivatives of U . Thus the intensive properties of the system are obtained by taking derivatives of the extensive property U with respect to extensive properties. It may be useful to consider the internal energy to be a function of T, P, and { n j } rather than S , and { n , ) ,but when that is done, it is not possible to calculate all the other thermodynamic properties of the system by taking partial derivatives. When U is expressed as a function of S , and { a , } , calculus requires that the total differential of U is given by

Comparison of equations 2.2-8 and 2.2-9 indicates that (2.2- 10) (2.2-11) (2.2- 12) The intensive variables T, P , and { p i ) can be considered to be functions of S, K and {q) because U is a function of S , r! and { q } .If U for a system can be determined experimentally as a function of S , r/; and { a , } , then 7; P , and ( p i } can be calculated by taking the first partial derivatives of U . Equations 2.2-10 to 2.2-12 are referred to as equations of state because they give relations between state properties at equilibrium. In Section 2.4 we will see that these N, + 2 equations of state are not independent of each other, but any N, + 1 of them provide a complete thermodynamic description of the system. In other words, if N , + 1 equations of state are determined for a system, the remaining equation of state can be calculated from the N , + 1 known equations of state. In the preceding section we concluded that the intensive state of a one-phase system can be described by specifying N , + 1 intensive variables. Now we see that the determination of N, 1 equations of state can be used to calculate these N, 1 intensive properties. The beauty of the fundamental equation for U (equation 2.2-8) is that it combines all of this information in one equation. Note that the N, + 2 extensive variables S, V and {ai) are independent, and the N , 2 intensive variables 7; P, and [pi} obtained by taking partial derivatives of U are dependent. This is wonderful, but equations of state 2.2-10 to 2.2-12 are not very useful because S is not a convenient independent variable. Fortunately, more useful equations of state will be obtained from other thermodynamic potentials introduced in Section 2.5. The fundamental equation for U is in agreement with the statement of the preceding section that for a homogeneous mixture of N, substances, the state of the system can be specified by N,+ 2 properties, at least one of which is extensive. The total number of variables involved in equation 2.2-8 is 2N, + 5. N, + 3 of these variables are extensive ( U , S, r/; and {ni}),and N, + 2 of the variables are intensive (7; P, {,ui}). Note that except for the internal energy, these variables appear in pairs, in which one property is extensive and the other is intensive; these are referred to as conjugate pairs. These pairs are given later in Table 2.1 in Section 2.7. When other kinds of work are involved, there are more than 2N, + 5 variables in the fundamental equation for U (see Section 2.7).

+

+

+

23

24

Chapter 2 Structure of Thermodynamics Equation 2.2-8 indicates that the internal energy U of the system can be taken to be a function of entropy S , volume V, and amounts { n , } because these independent properties appear as differentials in equation 2.2-8; note that these are all extensive variables. This is summarized by writing U ( S , V, ( n l ) ) . The independent variables in parentheses are called the natural variables of U. Natural variables are very important because when a thermodynamic potential can be determined as a function of its natural variables, all of the other thermodynamic properties of the system can be calculated by taking partial derivatives. The natural variables are also used in expressing the criteria of spontaneous change and equilibrium: For a one-phase system involving P V work, (dU) < 0 at constant S, U; and ini}. Fundamental equation 2.2-8 has been presented as the equation resulting from the first and second laws, but thermodynamic treatments can also be based on the entropy as a thermodynamic potential. Equation 2.2-8 can alternatively be written as 1 dS = - d U T

P

+ -dVT

p. c Adn, T N,

(2.2-13)

i=l

This fundamental equation for the entropy shows that S has the natural variables U,U; and {n,).The corresponding criterion of equilibrium is (dS) 2 0 at constant U , U; and { n , ) . Thus the entropy increases when a spontaneous change occurs at constant U, V, and (ni>.At equilibrium the entropy is at a maximum. When LJ, and { n , ) are constant, we can refer to the system as isolated. Equation 2.2-13 shows that partial derivatives of S yield 117; P J T and ,uI/T which is the same information that is provided by partial derivatives of U,and so nothing is gained by using equation 2.2-13 rather than 2.2-8. Since equation 2.2-13 does not provide any new information, we will not discuss it further. Equation 2.2-8 can be integrated at constant values of the intensive properties 7: P, and i n , } to obtain (2.2-14) This is referred to as the integrated form of the fundamental equation for U . Alternatively, equation 2.2-14 can be regarded as a result of Euler's theorem. A function f ( x 1, x2,. . . ,xN) is said to be homogeneous of degree n if

f ( k x , , kx,, . . . ,kx,)

= k"f(x,, x2,. . . ,x,)

(2.2-15)

For such a function, Euler's theorem states that (2.2-16) The internal energy is homogeneous of degree 1 in terms of extensive thermodynamic properties, and so equation 2.2-8 leads to equation 2.2-14. All extensive variables are homogeneous functions of the first degree of other extensive properties. All intensive properties are homogeneous functions of the zeroth degree of the extensive properties. Since integration introduces a constant, the value of U obtained from equation 2.2-14 is uncertain by an additive constant, but that is not a problem because thermodynamic calculations always involve changes in U , that is, A U .

2.3 MAXWELL EQUATIONS If the differential of a function f ( x , y ) given by df

=

Mdx

+ Ndy

(2.3-1)

2.4 Gibbs-Duhem Equation and the Phase Rule and the mixed partial derivatives are equal x

)

:

(

=

(E))

(2.3-2)

the function f is said to be exact, and the integral o f f is independent of path. If the mixed partial derivatives are not equal, the function ,f is said to be inexact, and the integral of the function is dependent on the path. In Section 2.2 it was noted that heat q and work w are inexact differentials because they depend on the path of integration. However, all state functions are exact differentials since they are independent of path of integration. Since the internal energy has an exact differential, equation 2.3-2 applies to its fundamental equation. In thermodynamics relations like equation 2.3-2 are referred to as Maxwell equations. For equation 2.2-2, the Maxwell equations are (2.3-3) (2.3-4) (2.3-5) (2.3- 6) Equations 2.2-10 to 2.2-12 and equations 2.3-3 to 2.3-6 show that the thermodynamic properties of a system are interrelated in complicated, and sometimes unexpected, ways. The next section shows that the intensive variables for a thermodynamic system are not independent of each other.

W

2.4 GIBBS-DUHEM EQUATION AND THE PHASE RULE

The differential of the integrated form (equation 2.2-14) of the fundamental equation for the internal energy is dU

=

T d S + P d T - PdV- VdP

+

N, I=

pldn, + 1

N,

i= 1

n,dpl

(2.4-1)

Subtracting the fundamental equation for U (equation 2.2-8) yields N,

SdT- V d P +

nidpi=O

(2.4-2)

i=l

which is referred to as the Gibbs-Duhem equation. This equation is important because it shows that the N , + 2 intensive properties for a homogeneous system without chemical reactions are not independent. But N , + 1 of them are independent. Note that this is in agreement with the experimental observation of Section 2.1 that the intensive state of a one-phase system can be specified by stating N , + 1 intensive variables. The Gibbs-Duhem equation is the basis for the phase rule of Gibbs. According to the phase rule, the number of degrees of freedom F (independent intensive variables) for a system involving only P V work, but no chemical reactions, is given by F

=

N, -p

+2

(2.4-3)

where p is the number of phases. This equation is derived in a more general form later in Chapter 8 on phase equilibria. Thus for a one-phase system without

25

26

Chapter 2 Structure of Thermodynamics chemical reaction, F = N , - 1 + 2 = N , + 1, as shown by equation 2.4-2. The independent intensive variables can be chosen to be 7: P, p , , . . . ,/ihrS-I or 7; ( p i or P, [pi]. Since F is the symbol for the number of independent intensive variables for a system, it is also useful to have a symbol for the number of natural variables for a system. To describe the extensive state of a system, we have to specify F intensive variables and in addition an extensive variable for each phase. This description of the extensive state therefore requires D variables, where D = F + p . Note that D is the number of natural variables in the fundamental equation for a system. For a one-phase system involving only PI/ work, D = N , + 2, as discussed after equation 2.2-12. The number F of independent intensive variables and the number D of natural variables for a system are unique, but there are usually multiple choices of these variables. The choice of independent intensive variables F and natural variables D is arbitrary, but the natural variables must include as many extensive variables as there are phases. For example, for the one-phase system described by equation 2.2-8, the F = N , 1 intensive variables can be chosen to be 7: P, .xl, x2,.. . ,xN-,and the D = N , + 2 natural variables can be chosen to be 7: P, n,, n2,. . . , nN,or 7: P. xi,xz,. . . , . Y , ~ , . , and n (total amount in the system).

I

+

2.5

LEGENDRE TRANSFORMS FOR THE DEFINITION OF ADDITIONAL THERMODYNAMIC POTENTIALS

The internal energy U has some remarkable properties and leads to many equations between the thermodynamic properties of a system, but S, V; and i n , ) are not convenient natural variables, except for an isolated system. As shown in Section 2.2, Legendre transforms can be used to introduce other sets of N , + 2 natural variables. A Legendre transform is a change in natural variables that is accomplished by defining a new thermodynamic potential by subtracting from the internal energy (or other thermodynamic potential) one or more products of conjugate variables. As mentioned after equation 2.2-2, examples of conjugate pairs are T and S, P and r/; and p, and n , . More conjugate pairs are introduced in Section 2.7. Callen (1985) emphasizes that no thermodynamic information is lost in making a Legendre transform. For reviews on Legendre transforms, see Alberty (1994d) and Alberty et al. (2001). Legendre transforms are also used in mechanics to obtain more convenient independent variables (Coldstein, 1980). The Lagrangian L is a function of coordinates and velocities, but it is often more convenient to define the Hamiltonian H with a Legendre transform because the Hamiltonian is a function of coordinates and momenta. Quantum mechanics is based on the Hamiltonian rather than the Lagrangian. In this section we will consider the Legendre transforms that define the enthalpy H , Helmholtz energy A , and Gibbs energy G. H=U+PV

(2.5-1)

A=U-TS

(2.5-2)

G = U + P V - TS

(2.5-3)

If a system can be described by d U = T d S - PdLc: there are only four thermodynamic potentials that can be defined in this way. We will consider only the equations for the Gibbs energy and the enthalpy. According to equation 2.5-3, the differential of G is given by dG

= dU

+ PdV+

VdP

--

TdS

-

SdT

(2.5-4)

2.5 Legendre Transforms for the Definition of Additional Thermodynamic Potentials Substituting equation 2.2-8 yields the fundamental equation for the Gibbs energy for a one-phase system without chemical reactions: N,

dG

=

-SdT+

VdP

+2

i= 1

,uidni

(2.5-5)

This shows that the natural variables of G for a one-phase nonreaction system are 7; P, and (n,}. The number of natural variables is not changed by a Legendre transform because conjugate variables are interchanged as natural variables. In contrast with the natural variables for U , the natural variables for G are two intensive properties and N , extensive properties. These are generally much more convenient natural variables than S. V, and {n,). Thus thermodynamic potentials can be defined to have the desired set of natural variables. It is important to understand that the change in variables provided by using a Legendre transform is quite different from the usual (much more frequent) type of change in variables. For example, in Chapter 1 functions of [H'] were converted to functions of pH by simply substituting [H'] = When a Legendre transform of a thermodynamic potential is defined, the new variable that is introduced is a partial derivative of that thermodynamic potential. For example, when U is known as a function of S , V, and { n , } ,the enthalpy is defined by use of H = U + PV= U + V(dU/dV),, and the natural variables of H are indicated by H ( S , -(dU/dV),) or H ( S , P). When the Gibbs energy is defined by use of G = U + P V - TS = U + V(dU/?V), - S (dU/dS)., and the natural variables of G are indicated by G((dU/dS) v , -(?U/dV),) or G(7; P). Since the natural variables of the Gibbs energy are 7; P, and { n , } , calculus yields

Comparison with equation 2.5-5 indicates that (2.5-7)

(2.5-8)

(2.5-9) Thus, if G can be determined as a function of 7; P , and { n i } , all of the thermodynamic properties of the system can be calculated. These N,+ 2 equations (that is equations 2.5-7 to 2.5-9) are often referred to as equations of state. Only N , + 1 equations of state are independent, and so if N, + 1 of them can be determined experimentally, the remaining equation of state can be calculated. The criterion of equilibrium for this one-phase system without chemical reactions is dG d 0 at constant 7; P, and (n,}. In other words, the Gibbs energy decreases in a spontaneous change in a system with constant T, P, and in,}.For this system the F = N, 1 independent intensive variables can be chosen to be 7; P, xl, x2,.. . , xN- and the D = N, 2 natural variables can be chosen to be 7; P , x l , x2,.. . , x N - l and n (total amount in the system), or 7; P , n,, n2,. . . ,n,,. The derivation in equations like 2.5-4 to 2.5-9 can be repeated for H and A . This shows that the natural variables for H are S , P , and ( n , } , and for A are 7; V, and { n L } . These thermodynamic potentials provide the following criteria for spontaneous change and equilibrium: dH < 0 at constant S, P , and ( n , ) ;dA < 0 at constant 7; and { n , } .

+

+

27

28

Chapter 2

Structure of Thermodynamics Substituting the integrated fundamental equation for U (equation 2.2-14) in the Legendre transforms defining H , A, and G shows that

+ Cp,n,

(2.5- 10)

-PV+ xprnr

(2.5-11)

H = TS

A

=

G

= C&n,

(2.5-12)

The interesting thing about these equations is that only the Gibbs energy G can be calculated by adding contributions from individual species. These thermodynamic potentials can be determined as functions of other variables, but only when they are determined as functions of natural variables can all of the thermodynamic properties be obtained by taking partial derivatives. Equations 2.5- 10 to 2.5-12 can also be obtained by integrating the corresponding fundamental equations at constant values of the intensive variables. The fundamental equation for the Gibbs energy (2.5-5) yields the following Maxwell equations: (2.5-13) (2.5- 14) (2.5-15) (2.5- 16) where S,(i) is the molar entropy of species i and V,(i) is its molar volume. The Helmholtz energy is not very useful as a crterion for spontaneious change and equilibrium in biochemistry because experiments are not done at constant volume. However, the enthalpy is important in biochemistry because it is connected with heat evolution and the change of the equilibrium constant with temperature. The fundamental equation for the enthalpy is N\

dH

=

TdS+PdV+

p,dn,

(2.5-17)

r = l

Since the enthalpy is defined by H = U + P I ! its total differential is d H = d U + P d V + VdP. Substituting the equation d U = d q - P d K given earlier in Section 2.2, yields d H = d q + VdP. At constant pressure the change in enthalpy AH is equal to the heat q absorbed by the system in the process, which may be irreversible. Thus thc change in enthalpy AH can be determined calorimetrically. The change in enthalpy can also be determined using the Gibbs-Helmholtz equation, which is introduced in the next paragraph, without using a calorimeter. Equations 2.5-1 and 2.5-3 show that G = H - TS. Substituting the expression for S from equation 2.5-7 yields (2.5-18) This is referred to as a Gibbs-Helmholtz equation, and it provides a convenient way to calculate H if G can be determined as a function of 7: P, and [ n r j .There is a corresponding relation between the internal energy U and the Helmholtz energy, which is defined by equation 2.5-2: (2.5-19) P In

This is also referred to as a Gibbs-Helmholtz equation.

;

2.5 Legendre Transforms for the Definition of Additional Thermodynamic Potentials Since G is additive in terms of p i (equation 2.5-12), S and H are also additive in terms of partial molar entropies and partial molar enthalpies, respectively: (2.5-20) The partial molar entropy Smiwas defined in equation 2.5-14. The additivity of the enthalpy can be seen by substituting equation 2.5-12 in equation 2.5-18: (2.5-21) where Hmiis the molar enthalpy of species i. Thus the chemical potential of a species is given by pi = H,i

-

(2.5-22)

TS,,

When a system at constant pressure is heated, it absorbs heat, and the heat capacity at constant pressure C , is defined by

Substituting equation 2.5-7 in H

c, =

(g)p

G

TS yields

=

H

=

-

G-T

(2.5-23)

(g)

(2.5-24)

P

Substituting this into the definition of C , yields

Thus we have seen that all the thermodynamic properties of a one-phase nonreaction system can be calculated from G( 7;P,(ni}). Although Legendre transforms introducing chemical potentials of species as natural variables are not discussed until Chapter 3, there is one Legendre transform involving chemical potentials of species that needs to be given here, and that is the complete Legendre transform U ' of the internal energy defined by U'

=

u

-

TS

+ PV-

c N S

(2.5-26)

,kini = 0

i=l

This transformed internal energy is equal to zero, as indicated by equation 2.2-8. The total differential of U' is 0 = dU

-

T d S + S d T + P d V + VdP

A',

1=

1 n,dpl N,

pldnl -

-

1

(2.5-27)

1=1

Substituting the fundamental equation for U yields the Gibbs-Duhem equation 2.4-2. Now we are in a position to generalize on the number of different thermodynamic potentials there are for a system. The number of ways to subtract products of conjugate variables, zero-at-a-time, one-at-a-time, and two-at-a-time, is 2k,where k is the number of conjugate pairs involved. In probability theory the number 2k of ways is referred to as the number of sets of k elements. For a one-phase system involving PV work but no chemical reactions, the number of natural variables is D and the number of different thermodynamic potentials is 2O. If D = 2 (as in d U = TdS - PdV), the number of different thermodynamic potentials is 22 = 4, as we have seen with U , H , A , and G. If D = 3 (as in dU = TdS - P dV + p dn), the number of different thermodynamic potentials is 23 = 8.

29

30

Chapter 2

Structure of Thermodynamics Thus the Gibbs-Duhem equation represents one of the 2D thermodynamic potentials that can be defined for a system, but this thermodynamic potential is equal to zero. It should be emphasized that there is a single Gibbs-Duhem equation for a one-phase system and that it can be derived from U , H , A , or G. When work other than PV work is involved in a system (see Section 2.7), Legendre transforms can be used to introduce intensive variables in addition to T and P as natural variables in the fundamental equation for the system. Each Legendre transform defines a new thermodynamic potential that needs a symbol and a name. Since every system has 2O possible thermodynamic potentials, and each needs a symbol and a name, nomenclature becomes a problem. Callen (1985) showed how each possible thermodynamic potential can bc given an unambiguous symbol. Callen nomenclature uses the symbol U [ . . . ] ,where ... is a list of the intensive variables introduced as intensive variables in dcfining the particular thermodynamic potential based on the internal energy. Thus the enthalpy H can be represented by U [ P ] , the Helmholtz energy A can be represented by U [ T ] , and the Gibbs energy G can be represented by U [ T , P ] . Since all possible thermodynamic potentials can be represented in this way, this is a good method to use when there is a possibility of confusion. However, in practice, it is convenient to use symbols like U ' , H ' , A', and G ' to represent transformed properties that are similar to U , H , A , and G. When this is done, it is important to specify which intensive properties have been introduced in defining these primed properties. The number of Maxwell equations for each of the possible thermodynamic potentials is given by D ( D - 1)/2, and the number of Maxwell equations for the thermodynamic potentials for a system related by Legendre transforms is [D(D - 1)/2]2D.Examples are given in the following section.

2.6 THERMODYNAMIC POTENTIALS FOR A SINGLE-PHASE SYSTEMS WITH ONE SPECIES The fundamental equation for U for a single-phase system with one species is dU

=

TdS

-

(2.6-1)

P d V + pdn

Integration of this fundamental equation at constant values of the intensive variables yields U

=

TS

+ PV+

(2.6-2)

pn

Since there are D = 3 natural variables, there are 23 - 1 = 7 possible Legendre transforms. The Legendre transforms defining H , A , and G are given in equations 2.5-1 to 2.5-3, and the four remaining Legendre transforms are U[p]= U

-

(2.6-3)

pn

U [ P , p ] = U + P V - pn

(2.6-4)

U [ T p ]= U

(2.6-5)

U[7;P,p]=

-

TS

-

u + PV-

pn TS

-

p/1= 0

(2.6-6)

These four Legendre transforms introduce the chemical potential as a natural variable. The last thermodynamic potential U [ T ,P , p ] defined in equation 2.6-6 is equal to zero because it is the complete Legendre transform for the system, and this Legendre transform leads to the Gibbs-Duhem equation for the system. Three of the eight thermodynamic potentials for a system with one species are frequently used in statistical mechanics (McQuarrie, 2000), and there are generally accepted symbols for the corresponding partition functions: U [ q = A = -RTln Q , where Q is the canonical ensemble partition function:

2.6 Thermodynamic Potentials for a Single-Phase Systems with One Species U [ 7 ; P ] = G = - R T l n A, where A is the isothermal-isobaric partition function; and U [ 7 ; p ] = -RTlnE, where E is the grand canonical ensemble partition function. When a system involves several species, but only one can pass through a membrane to a reservoir, U ( T , p l ] = - R T l n Y , where Y is the semigrand ensemble partition function. The last chapter of the book is on semigrand partition functions. Taking the differentials of the seven thermodynamic potentials defined above and substituting equation 2.6-1 yields the fundamental equations for these seven additional thermodynamic potentials:

+ VdP + pdn

(2.6-7)

dH

=

TdS

dA

=

-SdT-

dG

=

-SdT+ VdP

dU[p]

=

TdS - P d V - n d p

(2.6- 10)

dU[P,p]

=

TdS

+ VdP - n d p

(2.6-1 1)

dU[7;p]

=

-SdT-

PdV- ndp

dU[T,P,p]

=

-SdT+

VdP- n d p

PdV+ pdn

(2.6-8)

+ pdn

(2.6-9)

(2.6-1 2) =0

(2.6- 13)

This last equation is the Gibbs-Duhem equation for the system, and it shows that only two of the three intensive properties (7; P, and p) are independent for a system containing one substance. Because of the Gibbs-Duhem equation, we can say that the chemical potential of a pure substance substance is a function of temperature and pressure. The number F of independent intensive variables is F = 1 - 1 + 2 = 2, and so D = F + p = 2 + 1 = 3. Each of these fundamental equations yields D(D - 1)/2 = 3 Maxwell equations, and there are 24 Maxwell equations for the system. The integrated forms of the eight fundamental equations for this system are U(S,v n )

=

TS

H(S, P, n) = TS

-

P V + pn

+ pn

(2.6-14) (2.6-15)

A(7; v n ) = - P V + p n

(2.6-16)

G(7: P, n) = p n

(2.6-17)

U[p](S, K p ) = TS

UCP,PI(S, p ,

=

~

TS

WTpI(7; v p ) = - P V

u CT,P,PI(7; P , p ) = 0

PV

(2.6-18) (2.6-19) (2.6-20) (2.6-2 1)

where the natural variables are shown in parentheses. The basic question in all of thermodynamics is: A certain system is under such and such constraints, what is the equilibrium state that it can go to spontaneously? The amazing thing is that this question can be answered by making macroscopic measurements. Thermodynamics does not deal with the question as to how long it will take to reach equilibrium. We now have seven criteria for equilibrium in a one-phase system with one species and only P V work. The criteria of equilibrium provided by these thermodynamic potentials are (dU)s,",n d 0, (dH)S,P,n 0, (dA)T,",, d 0, (dG)*,P,nd 0, (d~CPl)s,v,fi d 0, ( d W P , PI)S,P,@d 0, and (d~CT,P1)T,v,fi d 0. The reason for going into this much detail on all of the thermodynamic potentials that can be defined for a one-phase, one-species system and the corresponding criteria for spontaneous change is to illustrate the process by which these thermodynamic potentials are defined and how they provide criteria for

31

32

Chapter 2 Structure of Thermodynamics

Table 2.1.

Conjugate Properties Involved in Various Kinds of Work Extensive

PV Chemical non rx system rx system Electrical Mechanical Surface Electric polarization Magnetic polarization

Intensive

V

-P

ni

Pi Pi

nci

-PdV Pidni Pi dnci 4; dQi .f dL 7 dAs E dP B dm

4i .f

Qi = Fzini

L AS

P

E B

m

Differential Work

spontaneity and equilibrium under various conditions. None of these equations is immediately applicable to biochemical reactions because they are for systems containing one species. Chemical reactions are introduced in the next chapter.

2.7 OTHER KINDS OF WORK In this chapter we have discussed systems involving P V work and the transfer of species into or out of the system ( p i dn,), but other kinds of work may be involved in a biochemical system. The extensive and intensive properties that are involved in various types of work are given in Table 2.1. Table 2.1, nCiis the amount of a component (see Section 3.3), qhi is the electric potential of the phase containing species i, Qi is the contribution of species i to the electric charge of a phase, zi is the charge number, F is the Faraday constant, ,f is force of elongation, L is length in the direction of the force, 7 is surface tension, A, is surface area, E is electric field strength, p is the electric dipole moment of the system, B is magnetic field strength (magnetic flux density), and rn is the magnetic moment of the system. Vectors are indicated by boldface type. If a single additional work term is involved, the fundamental equation for U is dU

=

TdS - VdP

+

N S

pidn,

+ XdY

(2.7-1)

i= 1

where Y is an extensive variable. This shows that D = N, + 3. The additional work terms should be independent of ( n i } because natural variables must be independent. The same form of work terms appear in the fundamental equations for H , A, and G. In order to introduce the intensive properties in other kinds of work as natural variables, it is necessary to use Legendre transforms.

2.8 CALCULATION OF THERMODYNAMIC PROPERTIES OF A MONATOMIC IDEAL GAS BY TAKING DERIVATIVES OF A THERMODYNAMIC POTENTIAL The treatments in the preceding sections have been pretty abstract, and it may be hard to understand statements like: Thus, if G can be determined as a function of T P , and { n i l , all of the thermodynamic properties of the system can be calculated” (which appeared after equation 2.5-9). However, there is one case where this can be demonstrated in detail, and that is for a monatomic ideal gas (Greiner, Neise, and Stocker, 1995). Statistical mechanics shows that the Gibbs energy of a monatomic ideal gas without electronic excitation (Silbey and Alberty,

2.8 Calculation of Thermodynamic Properties of a Monatomic Ideal Gas 2001) is given as a function of G

=

7: P, and n by 2nmkT

-nRTln

3/2

kT

(2.8-1)

where nz is the mass of the atom, k is the Boltzmann constant, and h is Planck's constant. Equations 2.5-7 to 2.5-9 show that S, and p can be calculated by taking partial derivatives of G with respect to 7: P, and n. Taking these partial derivatives yields S = nR (In

[(T)

2nmkT

3/2

+ ;)

kT

(2.8-2)

nRT P

I/= __

(2.8-3)

P= -RTh

[(T)

2nmkT

kT

3/2

(2.8-4)

Equation 2.8-2 is referred to as the Sackur-Tetrode equation. Since we have expressions for these three properties, we can calculate the properties U , H , A , and Cp:

H

=

U

=

A

=

C,

=

(;)

nRT

(i)

(2.8-5)

nRT

)'([

-nRTln

(g)

(2.8-6)

nmkT

3/2

kT

-

nRT

(2.8-7) (2.8-8)

nR

Note that U corresponds with the translational kinetic energy in three directions. Thus all the thermodynamic properties of an ideal monatomic gas can be calculated from G( 7; P , n). Equations 2.8-2 and 2.8-4 can be used to derive the expressions for the standard molar entropies and standard molar Gibbs energies of a monatomic gas: S,=Sz-Rln

(Fp)

(2.8-9)

-

(2.8-10)

where Pois 1 bar and

s:

=R

G:

= p' =

(In

[

2nmkT

-RTln

3/2

kT

+

;)

(2.8-1 1) (2.8- 12)

These are the properties of the monatomic gas at a pressure of 1 bar. It should be pointed out that this standard molar Gibbs energy is not the A,G" of thermodynamic tables because there the convention in thermodynamics is that the standard formation properties of elements in their reference states are set equal to zero at each temperature. However, the standard molar entropies of monatomic gases without electronic excitation calculated using equation 2.8-1 1 are given in thermodynamic tables.

33

34

Chapter 2

Structure of Thermodynamics Thus we have demonstrated the remarkable fact that equation 2.8-1 makes it possible to calculate all the thermodynamic properties for a rnonotomic ideal gas without electronic excitation. Here we have considered an ideal monatomic gas. but this illustrates the general conclusion that if any thermodynamic potential of a one-component system can be determined as a function of its natural variables, all of the thermodynamic properties of the system can be calculated.

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty Copyright 0 2003 John Wiley & Sons, Inc. ISBN 0-471-22851-6

3.1 Derivation of the Expression for the Equilibrium 3.2 3.3 3.4

Constant Changes in Thermodynamic Properties in Chemical Reactions Importance of Components Gibbs-Duhem Equation and the Phase Rule at Chemical Equilibrium

3.5 Isomer Group Thermodynamics 3.6 Effect of Ionic Strength on Equilibria in Solution Reactions

3.7 Effect of Temperature on Thermodynamic 3.8

Properties Chemical Thermodynamic Tables Including Biochemical Species

When a chemical reaction occurs in a closed system at constant T and P , the criterion for spontaneous change and equilibrium is no longer dG d 0 at constant 7; P , and (ni}because the amounts of species change in the reaction. Therefore, the following question arises: If the amounts of species are not constant during the approach to equilibrium in a reaction system, what is? The answer is: The amounts n,, of components are constant in a reaction system. When a chemical reaction occurs in a closed system, the amounts of atoms of elements and electric charge are conserved. Atoms of elements and electric charge can be taken as components, but some of these conservation equations may be redundant and are therefore not needed. Groups of atoms in molecules can also be chosen as components. This is important in biochemistry when large molecules are involved because counting atoms becomes laborious. Various choices of components can be made for a reaction system, but the number of components is independent of the set of components chosen. A particular set of components may be especially useful, depending on the objective of the calculation. In an independent set of conservation equations, no equation in the set can be obtained by adding and subtracting other equations in the set. Thus we will see in this chapter that the criterion for spontaneous change and chemical equilibrium in a closed system is

35

36

Chapter 3 Chemical Equilibrium in Aqueous Solutions dG < 0 at constant 7; P , and { n c l ) , where there are C components with amounts { n c l ) . Components are discussed in Section 3.3, and the various choices of components that can be used will become clearer in Chapter 5 on matrices. In this chapter we will find that when isomers are in chemical equilibrium, it is convenient to treat isomer groups like species in order to reduce the number of terms in the fundamental equation. We will also discuss the effect of ionic strength and temperature on equilibrium constants and thermodynamic properties of species. More introductory material on the thermodynamics of chemical reactions is provided in Silbey and Alberty (2001).

3.1

DERIVATION OF THE EXPRESSION FOR THE EQUILIBRIUM CONSTANT

When a chemical reaction occurs in a system, the changes in the amounts n, of species are not independent because of the stoichiometry of the reaction that occurs. A single chemical reaction can be represented by the reaction equation

1 viBi = 0 N,

(3.1-1)

i= 1

where Bi represents species i and N , is the number of different species. Chemical reactions balance the atoms of all elements and electric charge. The stoichiometric numbers vi are positive for products and negative for reactants. The amount ni of species i at any stage in a reaction is given by ni = nio

+ vij'

(3.1-2)

where nio is the initial amount of species i and j' is the extent of reaction. It is evident from this definition of 4 that it is an extensive property. Stoichiometric numbers are dimensionless, and so the extent of reaction is expressed in moles. The differential of the amount of species i is given by dni = vid(

(3.1-3)

When a single chemical reaction occurs in a closed system, the differential of the Gibbs energy (see equation 2.5-5) is given by dG

=

- S d T + VdP

+ C ti=,

pivi d(

,)

(3.1-4)

This form of the fundamental equation applies at each stage of the reaction. The rate of change of G with extent of reaction for a closed system with a single reaction at constant T and P is given by (3.1-5) where A,G is referred to as the reaction Gibbs energy. The Gibbs energy of the system is at a minimum at equilibrium, where (i?G/d()T,p= 0. At the minimum Gibbs energy, the equilibrium condition is (3.1-6) i= 1

Notice that this relation has the same form as the chemical equation (equation 3.1- 1).

3.1 Derivation of the Expression for the Equilibrium Constant To discuss equilibrium in a chemical reaction system, it is convenient to introduce the activity a, of a species to replace the chemical potential of a species because a, is more closely related to partial pressures and concentrations of species. The activity of a species is defined by p i = py

+ RTlna,

(3.1-7)

where $, which is referred to as the standard chemical potential, is the chemical potential when ai = 1. A superscript zero is used to designate a standard property, and so py is the standard chemical potential of species i. For ideal mixtures of ideal gases, ui can be replaced by P,/PO, where Po is the standard state pressure, and for ideal solutions a, can be replaced by ci/cO, where co is the standard concentration. Note that the activity a, of species i is dimensionless. We will use molar concentrations, but measurements in physical chemistry are frequently based on molal concentrations (mol kg- I). Molal concentrations m i have the advantage that they do not change with temperature. From one point of view nothing is gained by using equation 3.1-7 to define the activity aiof a species and using it to replace the chemical potential p i of the species. The difference between p i and ai is that p i of an ideal gas goes from - 00 to m, whereas a, goes from 0 to co. Thus the activity of a species in solution is more closely related to its concentration than pi is. However, the activity of a species in solution is directly proportional to its concentration only for ideal solutions. In general, the activity of a species in solution is given by a, = yici, where y i is the activity coefficient of species i. The activity coefficient of a solute is a function of the concentration, especially for ions. Strictly speaking (Mills et a]., 1993), this relation should be written a, = yici/cO, where c0 is the standard concentration (1 M). However, c0 is omitted in this book to simplify the equations. Thus equation 3.1-7 is written p i = pi0

+ RTlnyici

(3.1-8)

When using the molar concentration scale, the convention is that the activity coefficient of a species approaches unity as the concentration of the species approaches zero. In discussing biochemical reactions in dilute aqueous solutions, effects on activity coefficients arise primarily because of electrostatic interactions between charged species and depend on the ionic strength (see Section 1.2 and Section 3.6). Since the ionic strength is under the control of the investigator and is nearly constant during the approach to equilibrium when a biochemical reaction is carried out in dilute aqueous solution with a buffer, we can postpone discussing the effects of ionic strength to Section 3.6 by making the following observation: Equation 3.1-8 can be written p i=

,UP + RTIny, + RTlnci

(3.1-9)

In discussing biochemical thermodynamics, however, it is convenient to write this equation as p, =

+ RTlnc,

(3.1- 10)

where p j and are functions of the ionic strength. In equations 3.1-9 and 3.1-10, p , and p: have been used in two different ways, but in the rest of the book equation 3.1-10 will always be used. In other words, chemical potentials and other thermodynamic properties of species in dilute aqueous solutions will be taken to be functions of the ionic strength. This will allow us to avoid including y , in many places (even though the effect of ionic strength is taken into account) and to treat solutions at a specified ionic strength as “ideal solutions,” that is as solutions following equation 3.1-10. We have already seen an example of this in the treatment of pH in Section 1.2.

37

38

Chapter 3 Chemical Equilibrium in Aqueous Solutions Substituting equation 3.1-10 in 3.1-6 yields N*

N, i= 1

vipf = - R T

n (ci)ik NI

viln(ci)eq= -RTln

(3.1-11)

i= 1

i=l

Using the nomenclature of equation 3.1-5, equation 3.1-11 can be written as N S

A,Go

(3.1- 12)

viAfGY = -RTln K

= i=O

where A,G; is the standard reaction Gibbs energy and K is the equilibrium constant for a chemical reaction written in terms of species: (3.1- 13) ,= 1

An equilibrium constant must always be accompanied by a chemical equation. This equation is often used without the subscript "eq" that reminds us that the concentrations are equilibrium values. Strictly speaking, this equation should be written as K = lI(c,/cO)~;,but the standard concentration c0 = 1 M will be omitted, as mentioned before equation 3.1-8. Thus the equilibrium constant will be treated as a dimensionless quantity, as, of course, it must be if we are going to take its logarithm. When H,O is a reactant in a chemical reaction in dilute aqueous solutions, its molar concentration is not included in equation 3.1-13. The reason is that in reactions in dilute aqueous solutions the activity of water does not change significantly. The convention is that H,O is represented in the expression for the equilibrium constant by its activity, which is essentially unity independent of the extent of reaction. However, Af GO(H,O) is included in the calculation of A,Go using equation 3.1-12 and AfHO(H,O) is included in the calculation of A,Ho using equation 3.2-13, which is given later. To clarify the nature of the equilibrium state of a reaction system, consider the solution reaction A = B. When one liter of ideal solution initially containing A at 1 M is considered, the Gibbs energy of the reactants at any time is given by G

0

+ RTlnCA]) + n&; + RTln[B])

(3.1- 14)

= nA(pu,

Since nA = 1 - 4 and nB = 4, G = (1 - [ ) p i

+ ( p i + RT[(1

-

t ) l n ( l - (1 - 5))

+ 4In41

(3.1-15)

At the equilibrium state of the system, the Gibbs energy is at a minimum, and the equilibrium extent of reaction is teq.At (dG/d(), = 0, pi

-

p i = -RT1n(teq/(l - teq)) = -RTlnK

(3.1-16)

Figure 3.1 shows a plot of the Gibbs energy G of a reaction system A = B as a function of the extent of reaction when p i = 20 kJ mol - and = 18 kJ mol


)

(7.2-16)

Binding potentials n become more positive with increasing stability, in contrast to Gibbs energies of formation which become more negative. The values of Af G”’ and Fl agree for the tetramer because of the convention that AfG”(T) = 0. But for the dimer D, these two physical quantities are not equal as shown in the next section. In this section we have seen that in addition to the Af G‘’ for the various forms of the tetramer at a specified pH, the sum of various forms of the tetramer have AfG”’ values that are function of [O,].

7.3 PARTIAL DISSOCIATION OF TETRAMERS INTO DIMERS The tetramer (a2P2)of hemoglobin is partially dissociated into dimers ( 2 P ) . Mills, Johnson, and Ackers (1976) give the following value for the apparent equilibrium constant OK; (their symbol) for the association reaction in the absence of oxygen: (7.3.1) Therefore, since the standard transformed Gibbs energy of formation of T is taken as zero, the standard transformed Gibbs energy of formation of D is 30.083 kJ mol-’. The equilibrium constants for the dimer are given by D

+ 0, = D(OJ

D(0,) Since A,G’’(D)

+ 0, = D ( 0 2 ) 2 =

K;,

=

cD(02)1 CDICO2l

K;,

=

CD(02)21 = 8.155 x los CD(02)lCO21

=

3.253 x lo6

(7.3-2) (7.3-3)

30.08 kJ mol-’, A,G”O(D) is given by (Alberty, 1996b) A,G”’(D)

=

30.08 - R 7 l n P ,

(7.3-4)

127

128

Chapter 7 Thermodynamics of the Binding of Ligands by Proteins

Table 7.3

Standard Transformed Gibbs Energy of Formation A,G" and Standard Further Transformed Gibbs Energies of Formation A,G"O of Hemoglobin Dimer at 21.5'C, 1 bar, pH 7.4, [Cl-] = 0.2M, and 0.2M Ionic Strength A,G"'(TotD),'kJ mol [O,]

A,G"(TotD)/kJ molD D(O2) D(O,), A,G""(TotD)/kJ molArG"O(eq 7.3-4)/kJ mol K"(eq. 7.3-7)

30.083 25 9.447 23 -7.799 32 -

=5 x

lo-' M

[0,]=10-' M

30.083 25 23.250 50 19.807 30 19.240 4 -39.217 3 8.956 x lo6

33.772 6% 9.508 x lo'*

30.083 25 21.552 40 16.411 00 16.119 4 -35.053 7 1.637 x lo6

[02]=2x 1 0 P M 30.083 25 19.854 30 13.014 80 12.866 8 -33.802 7 0.982 x 10'

Source: Reprinted from R. A. Alberty, Biophys. Cliern. 62, 141-159 (1996), with permission from Elsevier Science. Note: See Problem 7.2.

The corresponding binding polynomial for dimer is given by P,

=

1

+ K;,[O,] + K;,[O,]'

(7.3-5)

Thermodynamic properties of dimmers are summarized in Table 7.3. The fractional saturation of dimer Y, is given by the Adair equation (see equation 7.1-18)

(7.3-6) The binding curve for dimer, which does not have a cooperative effect. is shown in Fig. 7.2. The fundamental equations for the dimer are similar to those for the tetramer. Table 7.3 gives AfG"' and A,G"'(TotD) at the same three oxygen concentrations as Table 7.1. The standard transformed Gibbs energies of formation of the three forms of the dimer are based on the convention that AfG"(T) = 0.

1x10"

2x10"

3x10"

4x 10 -I3

5x10"

Figure 7.2 Fractional saturation Y, of dimer with molecular oxygen calculated with the binding constants in equations 7.3-2 and 7.3-3 (see Problem 7.4).

7.4 Experimental Determination of Seven Apparent Equilibrium Constants The values of A,G"'(TotT) in Table 7.1 and AfG"'(TotD) in Table 7.2 make it possible to calculate the apparent equilibrium constant for the reaction 2TotD

= TotT

(7.3-7)

at three concentrations of molecular oxygen. The apparent equilibrium constant K " , which is a function of [O,], is defined by

K"

=

[TotT] [Tot D]

(7.3-8)

This apparent equilibrium constant can be written in terms of the binding polynomials of tetramer and dimer and "K';: (7.3-9) As [O,] approaches infinity, this apparent equilibrium constant approaches a limiting value because the reaction becomes 2D(02)2

(7.3-10)

= T(02)4

in the limit of infinite [O,]. The value of this apparent equilibrium constant at very high oxygen concentrations is given by

(7.3-11) Note that this equilibrium constant is 5 x lo4 times smaller than for 2D = T (see Problem 7.3). This is not unexpected because of the cooperative effect in the tetramer.

rn 7.4 EXPERIMENTAL DETERMINATION OF SEVEN APPARENT EQUILIBRIUM CONSTANTS The fractional saturation of tetramer Y, and the fractional saturation of dimer YD are functions only of [O,] at specified 7; P , pH, etc., as shown by equations 7.1-18 and 7.3-6. However, since the tetramer form is partially dissociated into dimers, the fractional saturation of heme Y is a function of both [O,] and [heme]. Ackers and Halvorson (1974) derived an expression for the function Y([O,], [heme]). When Legendre transforms are used, a simpler form of this function is obtained, and it can be used to derive limiting forms at high and low [heme]. These limiting forms are of interest because they show that if data can be obtained in regions where Y is linear in some function of [heme], extrapolations can be made to obtain Y, and Y,. These fractional saturations can be analyzed separately to obtain the Adair constants for the tetramer and the dimmer (Alberty, 1997a). When the tetramer and dimer are in equilibrium, the fractional saturation of heme is given by Y=fD%

(7.4-1)

+fTYT

where fD = 2[TotD]/[heme] is the fraction of the heme in the dimer and fT = 4[TotT]/[heme] is the fraction of the heme in the tetramer. Since fT = 1 - f,, equation 7.4-1 can be written

Y=

YT

+

fD( YD -

(7.4-2)

YT)

The concentration of heme in the solution is given by [heme]

= 2[TotD]

+ 4[TotT]

=

2[TotD]

+ 4K"[TotDI2

(7.4-3)

where equation 7.3-8 has been used in writing the last form. Applying the

129

130

Chapter 7 Thermodynamics o f the Binding of Ligands by Proteins quadratic formula shows that the equilibrium concentration of TotD is given by [TotD]

=

-2

+ (4 + 16K”[heme])”2 8K“

~

(7.4-4)

The fraction of heme in the dimer is given by

’’

2[To t D] = 2[TotD] 4[TotT] - 1

+

+

1 2K”[TotD]

(7.4-5)

Substituting equation 7.4-4 into equation 7.4-5 yields

.fD

2 = 1 + (1 + 4K”[heme])i71

(7.4-6)

Substituting this equation into equation 7.4-2 yields Y= Y,

Y,) + 1 + ( I 2(YD + 4K”[heme])’ -

(7.4-7)

At specified [O,], Y is a function only of [heme] in a way that is described by three parameters, Y,, Y,, and K“. This equation is the same as that derived by Ackers and Halvorson (1974), although it has a rather different form. If it were possible to titrate hemoglobin with oxygen at sufficiently high [heme], Y, could be obtained directly. However, for the values of the seven equilibrium constants obtained by Mills. Johnson, and Ackers (1976), the tetramer is partially dissociated at the highest practical heme concentrations of about 5 mM. Equation 7.4-7 indicates that if Y can be determined at several high [heme], a linear extrapolation is possible (see equation 7.4-12). As is evident from equation 7.4-7, the question as to whether [heme] is high or low depends on whether [heme] > bK” or [heme] < $K“. Of course, this criterion depends on [O,]. In considering plots of Y versus some function of [heme], [heme] = + K “ can be used to divide the dependence of Y on [heme] into high-heme and low-heme regions. If 4K”[heme] >> 1, equation 7.4-7 reduces to Y = Y,

+ (K”)1’2[heme]1 - ‘T)

(7.4-8)

Thus a plot of Y versus [heme]-”2 at a specified [O,] must approach linearity as [heme] is increased. The intercept of the limiting slope of a plot of Y versus at [hemel- ‘ I 2 = 0 is Y,, and the limiting slope is (Y, - Y,)/(K”)1i2. This slope is determined by two factors, (Y, - YT) and K The slope will be low at high [O,] because Y, - YT is small. The slope will be low at low [O,] because K “ is large. Once Y, has been determined at a series of [O,] by use of extrapolations of this type, Kk,, K&,, Kk3, and Kk4 can be calculated by the method of nonlinear least squares. The values of Y, at various [O,] can be determined by extrapolations at low [heme]. If 4K“[heme] 7/.is->.l. In writing chemical equations and biochemical equations it is important to be careful with names of reactants. Chemical reactions are written in terms of species. In chemical reaction equations, atoms of all elements and electric charges must balance. Biochemical reaction equations are written in terms of reactants, that is in terms of sums of species, H+is not included as a reactant and electric charges are not shown or balanced. In biochemical reaction equations, atoms of all elements other than hydrogen must balance. The names of the reactants that must be used in making calculations with this data base are given later. The program calctrGerx can be used to calculate the standard transformed Gibbs energy of reaction Ar G'" for a biochemical reaction in the form atp+h2o+de=adp+pi, where de is required for the Mathematica operation Solve. The desired pHs and ionic strengths can be specified. The program calckprime can be used to calculate the apparent equilibrium constant K for a reaction at desired pHs and ionic strengths. The program calctrGerx can also be used to calculate Af H'" by typing in a biochemical reaction in the form atph+h2oh+de=adph+pih. When oxidation and reduction are involved in an enzyme-catalyzed reaction, the standard apparent reduction potential for a half reaction can be calculated by typing the half reaction in calcappredpot and specifying the pHs and ionic strengths. The mathematical functions for the standard transformed Gibbs energies of formation of biochemical reactants contain information about the average number of hydrogen atoms bound, as mentioned above. The change in binding of hydrogen atoms in a biochemical reaction can be calculated by taking the difference between products and reactants, but in using Mathernatica there is an easier way and that is to take the derivative of Ar G'" with respect to pH: A, N H = (1/R7ln( lO))(dA, C'" /dpH) (3) The equilibrium composition for an enzyme-catalyzed reaction or a series of enzyme-catalyzed reactions can be calculated by using equcalcc or equcalccrx. The first of these programs requires a conservation matrix. The second requires a stoichiometric matrix. The second program is recommended, especially when water is involved as a reactant, because the convention that when dilute aqueous solutions are considered, the activity of water is taken to be unity, means that a second Legendre transform is necessary. This version of the package provides eleven additional programs. One of the prgrams calcdGHT makes it possible to take the effect of temperature into account if enthalpy data are available (ref. 6). The uses of these programs are illustrated in the notebook. Since the standard thermodynamic properties of adenosine have been determined (ref. 7), new values are given for the ATP series. These changes do not change the values of apparent equilibrium constants that are calculated between reactants in this series, but will be useful in investigating the production of adenosine.. The current table can be considerably extended by use of the compilations of Goldberg and Tewari of evaluated equilibrium data on biochemical reactions (ref. 8). Akers and Goldberg have published "BioEqCalc; A Package for Performing Equilibrium Calculations in Biohemical Reactions" (ref. 9). I am indebted to NIH 5-RO1-GM48358 for support of the research that produced these tables and to Robert A. Goldberg and Ian Brooks for many helpful discussions. References: 1. Alberty, R. A. Biophys. Chem. 1992 42, 117; 1992 43,239. 2. Alberty, R. A.; Goldberg, R. N. Biochemistry 1992 31, 10610. 3. Alberty, R. A. J. Phys. Chem. 1992 96, 9614. 4. Alberty, R. A. Arch. Biochem. Biophys. 1998 353, 116; 1998 358, 25. 5. Alberty, R. A. J. Phys. Chem. B 2001 105, 7865. 6. Boerio-Goates, J.; Francis, M. R.; Goldberg, R. N.; Ribeiro da Silva, M. A. V.; Ribeiro da Silva, M. D. M. C.; Tewari, Y. J. Chem. Thermo. 2001 33,929. 7. Goldberg, R. N. J. Phys. Chem. Ref. Data 1999 28, 931 and earlier articles in this series. 8. Akers, D. L.; Goldberg, R. N. Mathematicu J. 2001 8 , 1. (URL: http://www.mathematica-journal.com/issue/v8il/)

198

Mathernatica Solutions to Problems

ca1cdGmat::usage = "calcdQnat [speciesmat-] produces the function of pH and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species) at 298.15 K. The input speciesmat is a matrix that gives the standard Gibbs energy of formation, the standard enthalpy of formation, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the species. Energies are expressed in kJ mo1*-1."; calcdG3I::usage = "calcdG3I[reactantname-] produces the standard transformed Gibbs energies of formation at 298 K, pH 7, and ionic strengths of 0, 0.10, and 0.25 M. The reactant name calls a function of pH and ionic strength or a constant."; calcdG5pH::usage 11calcG5pH[reactantname-] produces the standard transformed Gibbs energies of formation at 298 K, ionic strength 0.25 M and p H s 5, 6, 7, 8, and 9. The reactant name calls a function of pH and ionic strength."; ca1cdHmat::usage = "calcdHmat[speciesmat-] produces the function of pH and ionic strength that gives the standard transformed enthalpy of formation of a reactant ( sum of species) at 298.15 K. The input is a matrix that gives the standard Gibbs energy of formation,the standard enthalpy of formation, the electric charge,and the number of hydrogen atoms in the species in the reactant. There is a row in the matrix for each species of the reactant. dhfnsp is a list of the functions for the species. Energies are expressed in kJ m01"-1."; calcdH3I::usage = m1calcdH31[reactanth-]produces the standard transformed enthalpies of formation at 298 K,pH 7,and ionic strengths of O,O.lO,and 0.25 M. The reactanth name calls a function of p H and ionic strength or a constant."; calcdH5pH::usage = lmcalcdHpH[reactanth-]produces the standard transformed enthalpies of formation at 298 K, ionic strength 0.25 M and pHs 5, 6, 7, 8, and 9. The reactanth name with hf calls a function of pH and ionic strength or a constant."; ca1ctrGerx::usage = E1calctrGerx[eg_,pHlist-,islist-] produces the standard transformed Gibbs energy of reaction in kJ mol"-l at specified p H s and ionic strengths for a biochemical equation typed in the form atp+ h2o+de==adp+pi. The names of the reactants call the corresponding functions of pH and ionic strength. pHlist and islist can be lists."; ca1ckprime::usage = "calckprime[e~,pHlist-,islist-] produces the apparent equilibrium constant K' at specified pHs and ionic strengths for a biochemical equation typed in the form atp+h2o+de==adp+pi. The names of the reactants call the corresponding functions of pH and ionic strength. pHlist and islist can be lists."; ca1cpK::usage = "CalCpK[SpeCieSmat_,no-,is-] calculates pKs of weak acids."; calcdGHT::usage= "calcdGHT[speciesmat-] calculates the effect of temperature on transformed thermodynamic properties."; "ca~cGeflsp[equat-,pH_rionstr-,z1-,nHl-] calcGef1sp::usage calculates the standard Gibbs energy of formation of the species of a reactant made up of a single species."; calcGef2sp::usage = 1 ' c a l c G e f 2 s p [ e q u a t ~ , p H _ , i o n s t r _ , z l ~ , n H l ~ , p K O ~ ] calculates the standard Gibbs energies of formation of the two species of a reactant made up of a two species."; calcGef3sp::usage = "ca~cGef3sp[eguat~,pH~,ionstr~,z1~,nHl~,pKlO~, pK201 calculates the standard Gibbs energies of formation of the three species of a reactant made up of a three species."; ca1cNHrx::usage = llcalcNHrx[eq-,pHlist-,islist-] calculates the change in binding of hydrogen ions in a biochemical reaction."; rxthermotab::usage = iirxthermotab[eq-,pHlist-,islist-] calculates a table of

BasicBiochemData2 standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in binding of hydrogen ions in a biochemical reaction."; round::usage= 1ground[vec-,params-:{4,2}] rounds to the desired number of digits."; mkeqm: :usage = llmkecpn[c-List,s-List] types out a biochemical reaction from its stoichiometric number vector."; nameMatrix::usage = "nameMatrix[m-List,s-List] types out the biochemical reactions in a system of biochemical reactions from the stoichiometric number matrix."; calcappredpot::usage= "CalCagpr~dgOt[~g_,nU~,pnlist~,islist~] calculates the standard apparent reduction potential of a half reaction at the desired pH and ionic strength."; equca1cc::usage = "equcalcc[as-,lnk-,no-] calculates the equilibrium composition for a biochemical reaction or a series of biochemical reactions, given the conservation matrix, a list of transformed Gibbs energies of formation, and a list of initial concentrations of reactants."; equca1crx::usage = llegucalcrx[nt-,lnkr-,no-] calculates the equilibrium composition for a biochemical reaction or a series of biochemical reactions, given the transposed stoichiometric number matrix, the apparent equilibrium constants of the reactons, and a list of initial concentrations of reactants."; listfnpHis::usage= "1istfnpHis is a list of functions, like atp, that gives the standard transformed Gibbs energies of formation of reactants."; 1istspeciesdata::usage = "listspeciesdata is a list of names, like atpsp, of data files on the species of a reactant."; listdG3I::usage= "listdG31 is a list of vectors, like atpis, that give the values of the standard transformed Gibbs energies of formation at pH 7 and 3 ionic strengths."; list::usage= "list is a list of names of reactants, each in quotation marks."; 1istreactantspH::usage = "listreactantspH is a list of vectors, like atppH,that give the values of the standard transformed Gibbs energy of formation of a reactant at 5 pH values."; listreactantsh::usage= "listreactantsh is a list of the names in quotation marks for the reactants for which the standard transformed enthalpy of formation is calculated."; 1isthisreactants::usage = "listhisreactants is a vector of the values of standard transformed enthalpies of formation of reactants at three ionic strengths."; listfnpHish::usage= "1istfnpHish is a function of pH and ionic strength that gives the standard transformed enthalpy of formation of a reactant."; 1istspeciesdatah::usage = "listspeciesdatah is a list of names, like atpsp, of data files on the species of a reactant for which the enthalpy is known."; 1isthpHreactants ::usage = "1isthpHreactants is a list of names of reactants, like atphpH, that give the values of the standard transformed enthalpy of formation at 5 pH values."; pH: :usage = "pH is an independent variable."; is::usage= "is is ionic strength, which is an independent variable."; atp::usage= "atp is the name of a reactant that yields a function of pH and ionic strength for the standard transformed Gibbs energy of formation."; atpsp::usage= "atpsp yields the basic data on the species of the reactant."; atpis::usage = "atpis yields the standard transformed Gibbs energy of a reactant at 3 values of the ionic strength."; atppH::USage = "atppH yields the standard transformed Gibbs energy of a reactant at 5 values of the ionic strength."; atph::usage= "atph yields the function of pH and ionic strength that gives the standard transformed enthalpy of formation of atp."; atphis::usage = "atphis yields the standard transformed enthaply of atp at 3 ionic strengths."; atphpH::usage = "atphis yields the standard transformed enthaply of at9 at 5 pH values."; tablel::usage= "table1 produces a table of standard transformed Gibbs energies of fonnation of reactants at pH 7 and ionic strengths of 0, 0.10, and 0.25 M.";

199

200

Mathematica Solutions to Problems table2::usage= "table2 produces a table of standard transformed Gibbs energies of formation of reactants at ionic strength 0.25 M and pHs of 5, 6, 7, 8, and 9."; table3::usage = "table3 produces a table of standard transformed enthalpies of formation of reactants at pH 7 and ionic strengths of 0 , 0.10, and 0.25 M."; table4::usage "table4 produces a table of standard transformed enthalgies of formation of reactants atonic strengths 0.25 M and gHs of 5, 6, 7 , 8, and 9."; Begin[ "BasicBiochemData2'Private' "1

BasicBiochemData2

I2.0

Basic data on the species that make up a reactant.

201

202

Mathematica Solutions to Problems

BasicBiochemData2

203

sorbosesp=({-911.95,-1263.3,0,12}}; succinatesg=i{-690.44,-908.68,-2,4},{-722.62,-908.84,-1,5},~-746.64,-912.2,0, 611; succinylcoAsp={{-509.72, -, -1, 41, {-533.76, -, 0, 511; sucrosesp={{-l564.7,-2199.87,0,22}}; thioredoxinoxsp=ii0,_,010)); thioredoxinredsp={(69.88,-,-2,0~,~20.56,-,-1,1~,~-25.37,-,0,2}); trygtophaneLsp={(-114.7,-405.2,0,12}}; tyrosineLsp=({-370.7,_,O,ll)); ubiguinoneoxsp={{O,-,O,90}}; ubiguinoneredsp=({-89.92,_,0,92)); uratesp={{-325.9,_,-1,3)}; ureasp={(-202.8,-317.65,0,41}; uricacidsp={{-356.9,-,0,4}}; valineLsp={{-358.65,-611.99,0,11}}; ~~1~~~~~~{{-750.49,-1045.94,0,10}}; XylUlOSeS~=~{-746.15.-1029.65,~,~~}};

These thermodynamic values are based on the usual conventions of chemical thermodynamic tables that Af Go = At H" = 0 for elements in defined reference states and for H + ( a = l ) . Additional conventions are that A f C o = AfH" = 0 for coA- , FAD,, 2 - , FADenz2-, cytochr~mec~',ferred~xin,,-~,FMN2-, glutathiomeox2-, NAD,, , NADP,, 3 - , retinal', thioredoxin,, O , and ubiquinoneOx0 .

-'

Calculation of the functions of pH and ionic strength for the standard transformed Gibbs energy of formation of reactants.

I3.0

calcdQnat [speciesmat-1 := Module[(dGzero, zi, nH, pHterm, isterm,gpfnsp),(*This program produces the function of pH and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species) at 298.15 K. The input speciesmat is a matrix that gives the standard Gibbs energy of formation, the standard enthalpy of formation, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the species. Energies are expressed in kJ rnol"-l.*) dGzero = speciesmat[[Al1,111; zi = speciesmat 1 [All,31 1 ; nH = speciesmat~[A11,411; pHterm = nH*8.31451*.29815*Log[1OA-pHI; isterm = 2.91482*((ziA2) nH)*(isA.5)/(1 + 1.6*isA.5); gpfnsp=dGzero pHterm - isterm; -8.31451*.298l5*Log[ApplyIPlus,Exg[-l*g~fnsp/(8.31451*.29815)11II

-

-

The following is a list of names of the reactants. After the calculation using calcdGmat, typing one of these names yields the function of pH and ionic strength that gives the standard transformed Gibbs energy of formation of the reactant at 298.15 K in dilute aqueous solution.

204

Mathematica Solutions to Problems

1iStfnpHi.S= (acetaldehyde, acetate, acetone, acetylcoA, acetylphos, aconitatecis, adenine, adenosine, adp, alanine, ammonia, amp, arabinose, asparaginel, aspartate, atp, bpg. butanoln, butyrate, citrate, citrateiso, COA, collglutathione, c02g, coatot, coag, cog, creatine, creatinine, cysteinel, cystinel, cytochromecox, cytochramecred, dihydroxyacetonephos, ethanol, ethylacetate, fadox, fadred, fadenzox, fadenzred. ferredoxinox, ferredoxinred, fmnox, fmnred, formate, fructose, fructose6phos. fructosel6phos, fumarate, galactose, galactoselphos, glucose, glucoselphos, glucose6phos, glutamate, glutamine, glutathioneox, glutathionered, glyceraldehydephos, glycerol, glycerol3phos, glycine, glycolate, glycylglycine, glyoxylate, h2ag, h2g, h20, h202aq, hydroxypropionateb, hypoxanthine, indole, ketoglutarate, lactate, lactose, leucineisol, leucinel, lyxose, malate, maltose, mannitolD, mannose, methaneaq, methaneg, methanol, methioninel, methylamineion, n2ag, nZg, nadox, nadred, nadpox, nadpred, 02agr 02g, oxalate, oxaloacetate, oxalosuccinate, palmitate, pep, pg2, pg3, phenylalaninel, pi, pgi, propanola, propanoh, pyruvate, retinal, retinol, ribose, riboselphos, ribose5pho6, ribulose, serinel, sorbose, succinate, succinylcoll, sucrose, thioredoxinox, thioredoxinred, tryptophanel, tyrosinel, ubiquinoneox, ubiquinonered, urate, urea, uricacid, valinel, xylose, xylulose};

The following is a list of names of the entries in the basic thermodynamic data on species making up a reactant. listspeciesdata = {acetaldehydesp, acetatesp, acetonesp, acetylcollsp, acetylphossp, aconitatecissp, adeninesp, adenosinesp, adpsp, alaninesp, ammoniasp, ampsp, arabinosesp, asparaginelsp, aspartatesp, atpsg, bpgsp, butanolnsp, butyratesp, citratesp, citrateisosp, coAsp, collglutathionesp, coagsp, co2totsg, coaqsp, cogsp, creatinesp, creatininesp, cysteinelsp, cystinelsg, cytochromecoxsp, cytochramecredsp, dihydroxyacetonephossp, ethanolsp, ethylacetatesp, fadoxsp, fadredsp, fadenzoxsp, fadenzredsp, ferredoxinoxsp, ferredoxinredsp, fmnoxsp, fmnredsp, formatesp, fructosesp, fructose6phossp, fructosel6phossp, fumaratesp, galactosesp, galactoselphossp, glucosesp, glucoselphossp, glucose6phossp, glutamatesp, glutaminesp, glutathioneoxsg, glutathioneredsp, glyceraldehydephossp, glycerolsp, glycerol3phossp, glycinesp, glycolatesp, glycylglycinesp, glyoxylatesp, haaqsp, hagsp, h2osp, h202aqsp, hydroxypropionatebsp, hypoxanthinesp, indolesp, ketoglutaratesp, lactatesp, lactosesp, leucineisolsp, leucinelsp, lyxosesp, malatesp,maltosesp, mannitolDsp, ma~osesp,methaneagsp,methanegsp, methanolsp, methioninelsp, methylamineionsp, naagsp, n2gsp, nadoxsp, nadredsp, nadpoxsp, nadpredsp, olagsp, 02gsp, oxalatesp, oxaloacetatesp, oxalosuccinatesp, palmitatesp, pepsp, pgasp, gg3sp, phenylalaninelsp, pisp, ppisp, propanol2sp, propanolnsp, pyruvatesp, retinalsp, retinolsp, ribosesp. riboselphossp, ribose5phossp. ribulosesp, serinelsp, sorbosesp, succinatesp, succinylcollsp, sucrosesp, thioredoxinoxsp, thioredoxinredsp, tryptophanelsp, tyrosinelsp, ubiquinoneoxsp, ubiguinoneredsp, uratesp, ureasp, uricacidsp, valinelsp, xylosesp, xylulosesp};

Now Map is used to apply calcdGmat to each of the matrices of species data.

BasicB ioc hemData2

205

Clear[acetaldehyde, acetate, acetone, acetylcoA, acetylphos, aconitatecis, adenine, adenosine, adp, alanine, ammonia, amp, arabinose, asparaginel, aspartate, atp, bpg, butanoln, butyrate, citrate, citrateiso, COA, coAglutathione, c02g, coatot, coag, cog, creatine, creatinine, cysteineb. cystinel, cytochromecox, cytochromecred, dihydroxyacetonephos, ethanol, ethylacetate, fadox, fadred, fadenzox, fadenzred, ferredoxinox, ferredoxinred, fmnox, fmnred, formate, fructose, fructose6phos. fructosel6phos, fumarate, galactose, galactoselphos, glucose, glucoselphos, glucose6phosr glutamate, glutamine, glutathioneox, glutathionered, glyceraldehydeghos, glycerol, glycero13phosr glycine, glycolate, glycylglycine, glyoxylate, haag, h2g, h20, h202ap, hydroxypropionateb, hypoxanthine, indole, ketoglutarate, lactate, lactose, leucineisol, leucinel, lyxose, malate, maltose, mannitolD, mannose, methaneaq, methaneg, methanol, methioninel, methylamineion, nlag, n2g, nadox, nadred, nadpox, nadpred, o2ag, 02g, oxalate, oxaloacetate, oxalosuccinate, palmitate, pep, pg2, pg3, phenylalaninel, pi, ppi, gropanol2, propanoln, pyruvate, retinal, retinol, ribose, riboselphos, ribose5phos, ribulose, serinel, sorbose, succinate, succinylcoA, sucrose, thioredoxinox, thioredoxinred, tryptophanel, tyrosinel, ubiguinoneox, ubiguinonered, urate, urea, uricacid, valinel, xylose, xylulose]; Evaluate[listfnpHis] = Map[calcdGmat, listspeciesdata] ;

The following shows an example of a function of pH and ionic strength for a reactant that gives the standard transformed Gibbs energy of formation.

0.5 0.5 -0.403393 (-2838.18 + (29.1482 is )/(1 + 1.6 i s ) -2.47897 Log [E 0.5

E

E

-0.403393 (-2811.48 + (11.6593 is -0.403393 (-2768.1

-

0.5

(11.6593 is

0.5

)/(1 + 1.6 is

0.5

)/(1 + 1.6 is

)

-

34.7056 Log[lO

- 32.2266 Log[lO

)

- 29.7477 Log[lO

-PH

-PH

-PH

I) +

])I

The value of the standard transformed Gibbs energy of formation of ATP at pH 7 and ionic strength 0.25 M can be calculated in kJ/mol as follows: atp/.pH->7/.is->.25

-2292.5

The values at pHs 6 , 7 , and 8 and at ionic strengths 0 and 0.25 M can also be calculated. atp/.pH->{6,7,8l/.is->{0,.251

{[-2366.43, -2363.76}, [-2292.61, -2292.51, {-2220.96, -2223.44))

I

206

Mathematica Solutions to Problems

a 4.0 Calculation of a table of standard transformed Gibbs energies of

formation of reactants at pH 7 and ionic strengths of 0, 0.10, and 0.25 M. calcdG3I[reactantname~]:=Module[{outl,out2,out3~,(*This program calculates the standard transformed Gibbs energies of formation at 298 K, pH 7, and ionic strengths of 0, 0.10, and 0.25 M. The reactant name calls a function of pH and ionic strength or a constant.*) outl=reactantname/.~pH-~7,is->O}; out2=reactantname/.{pH->7,is->.l}; out3=reactantname/.{gH->7,is->.Z5}; {outl,out2,out3~1;

This is a list of the three values to be calculated for each of the reactants. listdG3I = {acetaldehydeis, acetateis, acetoneis, acetylcoAis, acetylghosis, aconitatecisis, adenineis, adenosineis, adgis, alanineis, ammoniais, ampis, arabinoseis, asparaginelis, asgartateis, atgis, bggis, butanolnis, butyrateis, citrateis, citrateisois, coAis, collglutathioneis, coagis, coltotis, coaqis, cogis, creatineis, creatinineis, cysteinelis, cystinelis, cytochromecoxis, cytochromecredis, dihydroxyacetonephosis, ethanolis, ethylacetateis, fadoxis, fadredis, fadenzoxis, fadenzredis, ferredoxinoxis, ferredoxinredis, fmnoxis, fmnredis, formateis, fructoseis, fructose6phosis, fumaratel6ghosis, fumarateis, galactoseis, galactoselghosis, glucoseis, glucoselghosis, glucose6phosis, glutamateis, glutamineis. glutathioneoxis, glutathioneredis, glyceraldehydephosis, glycerol is , glycerol 3phosis , glycinei s , glycolat ei s , glycylglycinei 6 , glyoxylatei s , hlaqis, hlgis, h2ois, hlolaqis, hydroxypropionatebis, hypoxanthineis, indoleis, ketoglutarateis, lactateis, lactoseis, leucineisolis, leucinelis, lyxoseia, malateis, maltoseis, mannitolDis, mannoseis, methaneagis, methanegis, methanolis, methioninelis, methylamineionis, naaqis, nagis, nadoxis, nadredis, nadpoxis, nadpredis, olaqis, olgis, oxalateis, oxaloacetateis, oxalosuccinateis, palmitateis, pepis, pglis, pg3is, phenylalaninelis, piis, gpiis, proganollis, propanolnis, pyruvateis, retinalis, retinolis, riboseis, riboselphosis, ribose5phosis, ribuloseis, serinelis, sorboseis, succinateis, succinylcoAis, sucroseis. thioredoxinoxis, thioredoxinredis, tryptophanelis, tyrosinelis, ubiquinoneoxis, ubiquinoneredis, urateis, ureais, uricacidis, valinelis, xyloseis, xyluloseis);

Map is used to apply calcdG3I to each of the functions for reactants.

BasicBiochemData2

207

Clear[acetaldehydeis, acetateis, acetoneis, acetylcoAis, acetylphosis, aconitatecisis, adenineis, adenosineis, adpis, alanineis, ammoniais, ampis, arabinoseis, asparaginelis, aspartateis, atpis, bpgis, butanolnis, butyrateis, citrateis, citrateisois, coAis, colglutathioneis, coagis, coatotis, coaqis, cogis, creatineis, creatinineis, cysteinelis, cystinelis, cytochrmecoxis, cytochromecredis, dihydroxyacetonephosis, ethanolis, ethylacetateis, fadoxis, fadredis, fadenzoxis, fadenzredis, ferredoxinoxis, ferredoxinredis, fxnnoxis, fmnredis, formateis, fructoseis, fructose6phosis, fumaratel6phosis. fumarateis, galactoseis, galactoselphosis, glucoseis, glucoselphosis, glucose6phosis, glutamateis, glutamineis, glutathioneoxis, glutathioneredis, glyceraldehydeis, glycerolis, glycerol3phosis, glycineis, glycolateis, glycylglycineis, glyoxylateis, haaqis, hagis, hlois, h202agis. hydroxypropionatebis, hygoxanthineis, indoleis, ketoglutarateis, lactateis, lactoseis, leucineisolis, leucinelis, lyxoseis, malateis, maltoseis, mannitolDis, mannoseis, methaneaqis, methanegis, methanolis, methioninelis, methylamineionis, n2aqis. n2gis, nadoxis, nadredis, nadpoxis, nadpredis, oaaqis, oagis, oxalateis, oxaloacetateis, oxalosuccinateis, palmitateis, pepis, pgais, pg3is, phenylalanineLis, piis, ppiis, propanolais, propanolnis, pyruvateis, retinalis, retinolis, riboseis, riboselphosis, ribose5phosis, ribuloseis, serinelis, sorboseis, succinateis, succinylcoAis, sucroseis, thioredoxinoxis, thioredoxinredis, tryptophanelis, tyrosinelis, ubiguinoneoxis, ubiquinoneredis, urateis, ureais, uricacidis, valineLis, xyloseis, xyluloseis]; Evaluate[listdG31] = Map[calcdG31, listfnpHis] ; acetoneis I80.0378,

83.7102,

84.8958)

This is a list of the names of reactants. 1ist = { acetaldehyde , acetate , I' acetone *I, *I acety 1coA , acetylpho s , aconitatec is 'I , "adenine", "adenosine", nadpaa,"alanine", "ammonia", l l ~ p * "arabinose". , "asparagineL", "aspartateal,tlatpll, ltbpgml, "butanoln", "butyrate", "citrate", "citrateiso", I1coAn,"coAglutathione", llc02g~~,"co2totl1,I1coaqnl, licogii, "creatine", "creatinine", "cysteineL", f'cystineL1l, mmcytochromecoxll, "cytochromecred", "dihydroxyacetonephos", "ethanol", 'ethylacetate", "fadox", " f a d r ~ d ~"fadenzox", ~, " f adeazredlf,I 'ferredoxinox" , llferredoxinredll, I1 fmnoxll, llfmnredml, formate ' I , "fructoseB1,11fructose6phos 'I, "f ru~tosel6phos~~, "fumaratetV,"galactose1', "galactoselphos", I1glucosenl, "glUCOSelphOS", 1 1 g 1 ~ ~ o s e 6 p h ~"glutamatell, s11, llglutaminell, "glutathioneox", "glutathionered", "glyceraldehydephosll,llglycerolll, "glycerol3~hos",''glycine", llglycolate*l, "glycylglycine", "glyoxylatetl, 11h2ag11, "h2gIt,"h20", 11h202ag11, "hydroxypropionatebll,"hypoxanthineSf,"indole", 1actate It , 11 1act ose I' , 1euc ine isoL " , 1euc ineL *I, 1' 1yxo se , "ke tog lu tarate *I, "malatell,"maltose", %annitolD", 11mannose18, "methaneaq', "methaneg", iimethanol", "methionineL', "methylamineion", lmn2aq11, s1n2glm, "nadox", "nadred" , "nadpox", "nadpred", 1 1 0 2 a ~ 11102g11, 1, "oxalatelq,"oxaloacetate", lroxalosuccinatelm, llpalmitatel*, " p e p " r "pg2", "pg3", llphenylalanineL1l, lmpill, llppill, "propanol2", llpropanolnll. "retinal", "ribose". "riboselphosn, 1nribose5phos1i, "pyruvate'*,"retinall~, "ribulose", "serineL", lwsorboselv, "succinate'l, "succinylcoAwl,ilsucrosell, "thioredoxinox" , "thioredoxinredl', 'ltryptophaneLml, "tyrosineL1*,~gubiquinoneox", }; "ubiquinonered1*."urate" , lgurea","uricacid", "valineL", "xylose", iixyluloseii , I

1'

Table 1 Standard Transformed Gibbs Energies of Formation in kJ mol-' at 298.15 K, pH 7, and Ionic Strengths of 0, 0.10, and 0.25 M tablel=PaddedForm[TableForm[listdG3I,TableHead~ngs-~{list, {"I = 0 M1m,llI = 0.10 M","I = 0.25 M**)},TableSpacing->{.3,3)1,18,2)1

208

Mathematica Solutions to Problems

acetaldehyde acetate acetone acetylcoA acetylphos aconitatecis adenine adenosine adP alanine ammonia arabinose asparagineL aspartate atp bpg butanoln butyrate citrate citrateiso COA

coAglutathione c02g co2tot coaq cog creatine creatinine cysteineL cystineL cytochromecox cytochromecred dihydroxyacetonephos ethanol ethylacetate fadox fadred fadenzox fadenzred ferredoxinox ferredoxinred fmnox fmnred formate fructose fructose6phos fructoselbphos fumara te galactose galactoselphos glucose glucoselphos glucosebphos glutamate glutamine glutathioneox glutathionered glyceraldehydephos glycerol glycerol3phos glycine glycolate glycylglycine glyoxylate h2aq h2g h20 h202aq hydroxypropionateb hypoxanthine

[ = O M 20.83 -249.46 80.04 -60.49 -1109.34 -797.26 510.45 324.93 -1428.93 -91.31 80.50 -562.04 -342.67 -206.28 -456.14 -2292.61 -2202.06 227.72 -72.94 -963.46 -956.82 -7.98 563.49 -394.36 -547.33 -119.90 -137.17 100.41 256.55 -59.23 -187.03 0.00 -24.51 -1096.60 58.10 -18.00 1238.65 1279.68 1238.65 1229.96 0.00 38.07 759.17 800.20 -311.04 -436.03 -1321.71 -2202.84 -521.97 -429.45 -1317.50 -436.42 -1318.03 -1325.00 -377.82 -128.46 1198.69 625.75 -1088.94 -177.83 -1080.22 -180.13 -411.08 -200.55 -428.64 97.51 79.91 -157.28 -54.12 -318.62 249.33

I = 0.10 M 23.27 -248.23 83.71 -58.65 -1107.57 -800.93 513.51 332.89 -1425.55 -87.02 82.34 -556.53 -336.55 -201.38 -453.08 -2292.16 -2205.69 233.84 -69.26 -965.49 -958.84 -7.43 572.06 -394.36 -547.15 -119.90 -137.17 105.92 260.84 -55.01 -179.69 -5.51 -26.96 -1095.91 61.77 -13.10 1255.17 1297.43 1255.17 1247.71 -0.61 38.07 768.35 810.61 -311.04 -428.69 -1317.16 -2205.66 -523.19 -422.11 -1313.01 -429.08 -1313.34 -1320.37 -373.54 -122.34 1214.60 634.76 -1088.25 -172.93 -1077.83 -177.07 -409.86 -195.65 -428.64 98.74 81.14 -156.05 -52.89 -316.17 251.77

I = 0.25 M 24.06 -247.83 84.90 -58.06 -1107.02 -802.12 514.50 335.46 -1424.70 -85.64 82.93 -554.83 -334.57 -199.80 -452.09 -2292.50 -2207.30 235.82 -68.08 -966.23 -959.58 -7.26 574.83 -394.36 -547.10 -119.90 -137.17 107.69 262.22 -53.65 -177.32 -7.29 -27.75 -1095.70 62.96 -11.52 1260.51 1303.16 1260.51 1253.44 -0.81 38.07 771.31 813.97 -311.04 -426.32 -1315.74 -2206.78 -523.58 -419.74 -1311.60 -426.71 -1311.89 -1318.92 -372.15 -120.36 1219.74 637.62 -1088.04 -171.35 -1077.13 -176.08 -409.46 -194.07 -428.64 99.13 81.53 -155.66 -52.50 -315.38 252.56

BasicBiochemData2 indole ketoglutarate lactate lactose 1eucineisoL leucineL lyxose malate maltose manni tolD mannose me thaneaq methaneg methanol methionineL methylamineion n2aq n2g nadox nadred nadpox nadpred o2aq 02g oxalate oxaloacetate oxalosuccinate palmi tate Pep Pg2 Pg3 phenylalanineL

Pi PPi

propano12 propanoln pyruvate retinal retinol ribose riboselphos ribose5phos ribulose serineL sorbose succinate succinylcoA sucrose thioredoxinox thioredoxinred tryptophaneL tyrosineL ubiquinoneox ubiquinonered urate urea uricacid valineL xylose xylulose

503.49 -633.58 -316.94 -688.29 175.53 167.18 -349.58 -682.88 -695.65 -383.22 -430.52 125.50 109.11 -15.48 -63.40 199.88 18.70 0.00 1038.86 1101.47 163.73 229.67 16.40 0.00 -673.90 -713.38 -979.05 979.25 -1185.46 -1340.72 -1346.38 232.42 -1058.56 -1934.95 134.42 143.84 -352.40 1118.78 1170.78 -339.23 -1215.87 -1223.95 -336.38 -231.18 -432.47 -530.72 -349.90 -685.66 0.00 54.32 364.78 68.82 3596.07 3586.06 -206.03 -42.97 -197.07 80.87 -350.93 -346.59

507.78 -633.58 -314.49 -674.83 183.49 175.14 -343.46 -682.85 -682.19 -374.65 -423.18 127.94 111.55 -13.04 -56.67 202.94 18.70 0.00 1054.17 1115.55 173.52 235.79 16.40 0.00 -676.35 -714.60 -979.05 997.61 -1188.53 -1341.32 -1347.19 239.15 -1059.17 -1939.13 139.32 148.74 -351.18 1135.91 1189.14 -333.11 -1212.24 -1220.32 -330.26 -226.89 -425.13 -530.65 -348.06 -672.20 0.00 55.41 372.12 75.55 3651.15 3642.37 -204.81 -40.53 -194.63 87.60 -344.81 -340.47

509.16 -633.58 -313.70 -670.48 186.06 177.71 -341.48 -682.85 -677.84 -371.89 -420.81 128.73 112.34 -12.25 -54.49 203.93 18.70 0.00 1059.11 1120.09 176.68 237.77 16.40 0.00 -677.14 -715.00 -979'.05 1003.54 -1189.73 -1341.79 -1347.73 241.33 -1059.49 -1940.66 140.90 150.32 -350.78 1141.45 1195.07 -331.13 -1211.14 -1219.22 -328.28 -225.51 -422.76 -530.64 -347.47 -667.85 0.00 55.74 374.49 77.73 3668.94 3660.55 -204.41 -39.74 -193.84 89.78 -342.83 -338.49

5.0 Calculation of a table of standard transformed Gibbs energies of

reactants at pH 5, 6, 7, 8, and 9 and ionic strength 0.25 M

209

210

Mathematica Solutions to Problems calcdG5~H[reactantn~e~]:=Module[{outl,out2,out3,out4,out5},(*This program calculates the standard transformed Gibbs energies of formation at 298 K, ionic strength 0.25 M and pHs 5, 6, 7, 8, and 9. The reactant name calls a function of pH and ionic strength.*) outl=reactantname/.CpH->S,is->.25}; out2=reactantname/.{pH->6,is->.25]; out3=reactantname/.{pH->7,is->.25}; out4=reactantname/.{pH->8,is->.25}; out5=reactantname/.{pH->9,is->.25]; {outl,out2,out3,out4,0ut5~1;

This is a list of the values to be calculated for each of the reactants. listreactantspH= {acetaldehydepH, acetatepH, acetonepH, aCetylCOApH, acetylphospH, aconitatecispH, adeninepH, adenosinepH, adppH, alaninepH, ammoniapH, amppH, arabinosepH, asparagineLpH, aspartatepa, atppH, bpgpH, butanohpH, butyratepH, citratepH, citrateisops, C O A ~ H ,coAglutathionepH, CO2gpH, CoatOtpH, COagpH, cogpH, creatinepH, CreatininepH, CySteineLpH, cystineLpH, cytochromecoxpH, cytochrmecredpH, dihydroxyacetonephospH, ethanolpH, ethylacetatepH, fadoxpH, fadredpH, fadenzoxpH, fadenzredps, ferredoxinoxpH, ferredoxinredpa, fmnoxpH, fmnredpH, formatepH, fructosepH, fructose6phospH. fructosel6phospH. fUnLaratepH, galactosepH, galactoselphospH, glucosepH, glucoselphospH, glucose6phospH, glutamatepa, glUtamin0pH. glutathioneoxpH, glutathioneredpa, glyceraldehydephospH, glycerolpH, glYCerOl3ghOSpHr glycinepH, glycolatepH, glyCylglyCinepH, glyOxyhtepH, h2aqpH, h2gpH. h2opH, h202aqpH, hydroxypropionatebpH. hypoxanthinepH, indolepH, ketoglutaratepa. lactatepH, hCtOSepH, leucineisoLpH, IeucineLpH, 1yxosepH. malatepH, maltosepH, maMitOlDpH, mannosepH, methaneaqpa, methanegpH, methanolpH, methionineLpH, methylamineionpH, n2agpH, nZgpH, nadoxpH, nadredpH, nadpoxpH, nadpredpH, o2aqpH, o2gpH, OXaht0pH, OxaloacetatepH, OXalOSUCCinatepH, palmitatepH, peppH. pglpH, pg3pH. phenylalanineLpH, pipH, ppipH, propanol2pH, prOpanOhpH, pyruvatepH, retinalga, retinolpH, ribosepH, riboselphospH, ribose5phospH, ribulosepH, SerineLpH, sorbosepH, SUCCinatepH. succinylcoApH, sucrosepH, thioredoxinoxpH, thioredoxinredpa, tryptophaneLpH, tyrosineLpH, ubiguinoneoxpH, ubiquinoneredpH, uratepH, ureapH, uricacidpH, valineLpH, xylosepH, xylulosepH};

Map is used to apply calcdG5pH to each of the functions for the reactants. Clear[acetaldehydepH, acetatepH, acetonepH, acetylcoApH, acetylphospH, aconitatecispH, adeninepH, adenosineps, adppH, alaninepH, ammoniapH, amppH, arabinosepa, asparaginelpH, aspartatem, atppa, bpgpH, butanolnpH, butyratepH, citratepH, citrateisopH. C O A ~ H ,coAglutathionepH, co2gpH, co2totpHr coaqpH, cogpH, creatinepH, creatininepa, CysteineLpH, CystineLpH, cytochramecoxpH, cytochromecredpH, dihydroxyacetonephospH, ethanolpH, ethylacetatepa, fadoxpH, fadredpH, fadenzoxpH, fadenzredps, ferredoxinoxpH, ferredoxinredpa, fmnoxpH, fmnredpH, formatepH, fructosepH, fructose6phospH, fructosel6phospH. fumaratepH, galactosepH, galactoselphospH, glucosepH, glucoselphospH, gluCoSe6phoSpHr glutamatepH, glutaminepH, glutathioneoxpH, glutathioneredpa, glyceraldehydephcspH, glycerolpH, glycerol3phospH, glYCinepH, glycolatepH, glycylglycinepH, glyOxylatepH, h2aqpHr hagpH, h2opH, h202aqpH, hydroxypropionatebpH, hypoxanthinepn, indolepH, ketoglutaratepa, lactatepH, hCtOSepH, 1eucineisoLpH. leucineLpH, 1yxosepH. malatepH, maltosepH, rnaMitolDpH, mannoSepH, methaneapga, methanegpa, methanolpH, methionineLpH, methylamineionpH, nZagpH, nagpH, nadoxpH, nadredpH, nadpoxgH, nadpredpH, 02aqpH, o2gpH, oxalatepH, oxaloacetatepH, oxalosuccinatepH, palmitatepH, pepgH, pglpH, pg3pH, RhenylalanineLpH, pipH, ppipH, prOpan012pH. propanolnpH, RYruVatepH, retinalpH, retinolpH, ribosepH, riboselphospH, ribose5phospHr ribulosepH, SerineLpH, sorbosepa, SuccinatepH, succinylcoApH, sucrosepH, thioredoxinoxpH, thioredoxinredpH, tryptoghaneLpH, tyrosinelpH, ubiguinoneoxpH, ubiquinoneredps, UratepH. ureapH, UricacidpH, ValineLQH, xylosepH, xylulosepH];

BasicBiochemData2

211

Evaluate [listreactantspH] = Map[calcdGSpH, listfnpHis] ;

Table 2 Standard Transformed Gibbs Energies of Formation of Reactants at 298.15 K, Ionic Strength 0.25 M, and pHs of 5 , 6,7, 8, and 9 table2nPaddedForm [TableForxn[ listreactantsps,TableHeadings - > { list, { "pH 5 #I, "pH 6 " , "pH 7'1, "pH 8 " , "pH 9")1, Tablespacing->{ .3,2 1 1 ,{ 6 , 2 ) 1

acetaldehyde acetate acetone acetylcoA acetylphos aconitatecis adenine adenosine adp alanine ammonia amp arabinose asparagineL aspartate atP bpg butanoln bu tyrate citrate citrateiso coA coAglutathione c02g co2tot coaq cog creatine creatinine cysteineL cystineL cytochromecox cytochromecred dihydroxyacetonephos ethanol ethylacetate fadox fadred fadenzox fadenzred ferredoxinox ferredoxinred fmnox fmnred formate fructose fructose6phos fructosel6phos fumarate galactose galactoselphos glucose glucoselphos glucose6phos g1utamate glutamine glutathioneox glutathionered glyceraldehydephos g1ycero1 glycerol3phos

PH 5 -21.60 -282.71 16.40 -92.31 -1153.77 -836.37 457.06 186.98 -1569.05 -165.55 37.28 -698.40 -448.73 -291.13 -520.59 -2437.46 -2262.15 121.66 -147.99 -1027.23 -1020.58 -18.48 403.59 -394.36 -564.61 -119.90 -137.17 4.95 182.31 -133.37 -314.31 -7.29 -27.75 -1154.88 -5.54 -102.85 906.61 926.43 906.61 876.71 -0.81 38.07 554.41 574.23 -322.46 -563.31 -1445.66 -2326.42 -546.67 -556.73 -1440.96 -563.70 -1442.86 -1449.53 -463.48 -234.52 877.26 455.34 -1147.22 -262.68 -1163.24

PH 6 1.23 -265.02 50.65 -75.19 -1129.84 -819.24 485.92 261.25 -1495.55 -125.59 60.11 -625.22 -391.65 -245.47 -486.34 -2363.76 -2233.92 178.74 -108.03 -995.44 -988.80 -12.79 489.21 -394.36 -554.49 -119.90 -137.17 56.32 222.27 -93.43 -245.81 -7.29 -27.75 -1124.53 28.71 -57.19 1083.56 1114.79 1083.56 1065.07 -0.81 38.07 662.86 694.10 -316.75 -494.81 -1379.42 -2264.57 -535.02 -488.23 -1375.09 -495.20 -1376.01 -1382.88 -417.82 -177.44 1048.50 546.64 -1116.87 -217.02 -1118.83

PH 7

24.06 . -247.83 84.90 -58.06 -1107.02 -802 12 514.50 335.46 -1424.70 -85.64 82.93 -554.83 -334.57 -199.80 -452.09 -2292.50 -2207.30 235.82 -68.08 -966.23 -959.58 -7.26 574.83 -394.36 -547.10 -119.90 -137.17 107.69 262.22 -53.65 -177.32 -7.29 -27.75 -1095.70 62.96 -11.52 1260.51 1303.16 1260.51 1253.44 -0.81 38.07 771.31 813.97 -311.04 -426.32 -1315.74 -2206.78 -523.58 -419.74 -1311.60 -426.71 -1311.89 -1318.92 -372.15 -120.36 1219.74 637.62 -1088.04 -171.35 -1077.13 ~

PH 8 46.90 -230.70 119.14 -40.94 -1085.39 -785.00 543.04 409.66 -1355.78 -45.68 105.64 -486.04 -277.49 -154.14 -417.85 -2223.44 -2183.36 292.90 -28.12 -937.62 -930.97 -2.82 660.45 -394.36 -541.18 -119.90 -137.17 159.07 302.18 -14.97 -108.82 -7.29 -27 .I5 -1067.13 97.20 34.14 1437.46 1491.52 1437.46 1441.80 -0.81 38.07 879.77 933.84 -305.34 -357.82 -1252.84 -2149.62 -512.16 -351.24 -1248.72 -358.21 -1248.92 -1255.98 -326.49 -63.28 1390.98 726.89 -1059.47 -125.69 -1036.91

PH 9 69.73 -213.57 153.39 -23.81 -1066.49 -767.87 571.58 483.87 -1287.24 -5.73 127.51 -417.51 -220.41 -108.47 -383.60 -2154.88 -2160.38 349.98 11.83 -909.07 -902.42 -1.10 746.07 -394.36 -535.80 -119.90 -137.17 210.44 342.13 20.99 -40.33 -7.29 -27.75 -1038.59 131.45 79.81 1614.40 1679.89 1614.40 1630.17 -0.81 38.07 988.22 1053.70 -299.63 -289.33 -1190.04 -2092.54 -500.74 -282.75 -1185.93 -289.72 -1186.11 -1193.18 -280.82 -6.20 1562.22 813.52 -1030.93 -80.02 -996.93

212

Mathematica Solutions to Problems

glycine glycolate glycylglycine glyoxylate h2aq h2g h20 h202 aq hydroxypropionat.eb hypoxanthine indole ketoglutarate lactate lactose 1eucineisoL leucineL lyxose malate ma 1t0 s e manni to1D manno s e me thaneaq methaneg methanol methionineL methylamineion n2aq n29 nadox nadred nadpox nadpred o2aq 029 oxalate oxaloacetate oxalosuccinate palmi tate Pep P92 Pg 3 phenylalanineL Pi PPi propano12 propanoln pyruvate retinal retinol ribose riboselphos ribose5phos ribul ose serineL sorbose succinate succinylcoA sucrose thioredoxinox thioredoxinred tryptophaneL tyrosineL ubiquinoneox ubiquinonered urate urea uricacid valineL xylose xylulose

-233.16 -443.71 -285.40 -440.06 76.30 58.70 -178.49 -75.33 -372.46 206.90 429.25 -679.25 -370.78 -921.63 37.65 29.30 -455.64 -729.49 -928.99 -531.71 -557.80 83.07 66.68 -57.91 -180.07 135.43 18.70 0.00 762.29 811.86 -108.72 -59.05 16.40 0.00 -677.26 -737.83 -1024.72 649.64 -1218.97 -1396.52 -1402.06 115.75 -1079.46 -1957.07 49.57 58.99 -385.03 821.80 852.59 -445.29 -1320.16 -1328.24 -442.44 -305.42 -559.75 -578.32 -393.33 -919.00 0.00 33.33 237.50 -47.85 2641.49 2610.27 -238.66 -85.40 -239.50 -35.80 -456.99 -452.65

--204.62 --426.59 -239.74 -434.35 87.72 70.12 -167.07 -63.91 -343.92 229.73 469.21 -656.42 -342.24 -796.06 111.85 103.50 -398.56 -705.79 -803.42 -451.80 -489.30 105.90 89.51 -35.08 -117.28 169.68 18.70 0.00 910.70 965.98 33.98 89.36 16.40 0.00 -677.15 -726.41 -1001.89 826.59 -1203.00 -1368.31 -1373.94 178.54 -1068.49 -1947.46 95.23 104.65 -367.91 981.62 1023.83 -388.21 -1264.30 -1272.38 -385.36 -265.46 -491.25 -553.72 -370.32 -793.43 0.00 44.70 306.00 14.94 3155.21 3135.41 -221.54 -62.57 -216.67 26.99 -399.91 -395.57

-176.08 -409.46 -194.07 -428.64 99.13 81.53 -155.66 -52.50 -315.38 252.56 509.16 -633.58 -313.70 -670.48 186.06 171.71 -341.48 -682.85 -677.84 -371.89 -420.81 128.73 112.34 -12.25 -54.49 203.93 18.70 0.00 1059.11 1120.09 176.68 237.77 16.40 0.00 -677.14 -715.00 -979.05 1003.54 -1189.73 -1341.79 -1347.73 241.33 -1059.49 -1940.66 140.90 150.32 -350.78 1141.45 1195.07 -331.13 -1211.14 -1219.22 -328.28 -225.51 -422.76 -530.64 -347.47 -667.85 0.00 55.74 374.49 77.73 3668.94 3660.55 -204.41 -39.74 -193.84 89.78 -342.83 -338.49

-147.54 -392.34 -148.41 -422.94 110.55 92.95 -144.24 -41.08 -286.84 275.40 549.12 -610.75 -285.16 -544.90 260.26 251.91 -284.40 -660.00 -552.26 -291.97 -352.31 151.57 135.18 10.59 8.29 23.8.17 18.70 0.00 1207.51 1274.21 319.38 386.18 16.40 0.00 -677.14 -703.58 -956.22 1180.48 -1178.02 -1317.92 -1324.05 304.11 -1052.97 -1935.64 186.56 195.98 -333.66 1301.27 1366.31 -274.05 -1159.50 -1167.58 -271.20 -185.55 -354.26 -507.79 -324.63 -542.27 0.00 64.03 442.99 140.51 4182.66 4185.69 -187.29 -16.90 -171.00 152.56 -285.75 -281.41

-119.00 -375.21 -102.74 -417.23 121.96 104.36 -132.83 -29.67 -258.30 298.23 589.07 -587.92 -256.62 -419.32 334.47 326.12 -227.32 -637.17 -426.68 -212.06 -283.82 174.40 158.01 33.42 71.08 272.42 18.70 0.00 1355.92 1428.33 462.08 534.59 16.40 0.00 -677.14 -692.16 -933.39 1357.43 -1166.58 --1294.95 -1301.11 366.90 -1047.17 -1933.29 232.23 241.65 -316.53 1461.10 1537.55 -216.97 -1108.09 -1116.17 -214.12 -145.60 -285.77 -484.95 -301.80 -416.69 0.00 66.35 511.48 203.30 4696.38 4710.83 -170.16 5.93 -148.17 215.35 -228.67 -224.33

BasicBiochemData2

213

6.0 Calculation of the functions of pH and ionic strength for the standard

transformed enthalpies of formation of reactants calcdmat [speciesmat-] := Module[(dHzero, zi, nH, dhfnsp, dGzero, pHterm, isenth, dgfnsp, doreactant, ri), (*This program produces the function of ionic strength (is) that gives the standard transformed enthalpy of formation of a reactant (sum of species) at 298.15 K. The input is a matrix that gives the standard Gibbs energy of formation, the standard enthalpy of formation, the electric charge, and the number of hydrogen atoms in the species in the reactant. There is a row in the matrix for each species of the reactant. dhfnsp is a list of the functions for the species. Energies are expressed in kJ mol"-l.*) dHzero = speciesmat [ [All, 21 ] ; zi = speciesmat [ [All, 31 ]; n H = speciesmat[[All, 411; isenth=1.4775* ((zi"2) -nH) * (isA.5) / (1+1.6*isA.5); dhfnsp = dlizero+isenth; (*Now calculate the functions for the standard Gibbs energies of formation of the species.*) dGzero = speciesmat [ [All, 11 ]; pHterm = nH * 8.31451 * .29815 * Log [ 10 A - pH] ; gpfnsp = dGzero pHterm - isenth * 2.91482 / 1.44775; (*Now calculate the standard transformed Gibbs energy of formation for the reactant.*) dGreactant = -8.31451* .29815*Log[Apply[Plus, Exp[-l*gpfnsp/ (8.31451* .29815)]]]; (*Now calculate the equilibrium mole fractions of the species in the reactant and the mole fraction-weighted average of the functions for the standard transformed enthalpies of the species.*) ri = Exp[ (dGreactant gpfnsp) / (8.31451 * .29815)1 ; ri.dhfnsp]

-

-

The following is a list of functions for the reactants with which the standard transformed enthalpies of formation can be calculated. It is shorter than the list of reactants for the transformed Gibbs energies because these is less information about standard enthalpies of formation of species. listreactantsh={"acetaldehyde", "acetate", "adenosine",lladpml, "alanine", rgammonia 'I, I I a m p " , l*arabinose", "asparagineL",llaspartatell, lvatpil, "citrate","c02g1',"c02tot", IIcoaq", "C ogl', "ethanol11, "ethylacetate","formateml, "fructose",r l f ~ r a t e ""galactose", , "glucose", "glu cose6phos", "glutamatell, "glutaminemt, lrglycerollr, l'glycinell, Eiglycylglycineii, Irh2aq","h2g","h 20", 'th202aq1t, "indole","lactate",lvlactosela, "leucineL","maltose",19nannose","methaneg","me thaneaq" ,"methanol",ilmethylamineionrl, iin2aql*, **n2gra, tlnadox*l, "nadpox" ,"nadpred" ,%adred", '' 02aq", 1102g~~, "pi", "ppi",11propano12", iipyruvatei', "ribose","ribose5phos", "ribulose", "sorbos ell, "succinate","sucroset1, "tryptophaneL1'."urea", lsvalineL'l, "xylose", "xylulosetm) ;

214

Mathematica Solutions to Problems listfnpHish={acetaldehydeh,acetateh,acetoneh,adenosineh,adgh,alanineh,ammoniah,amgh,ara binoseh,asparagineLh,aspartateh, atph,citrateh,coagh, coatoth, coaqh, cogh, ethanolh, ethylacetateh, formateh, fructoseh, fumarateh, galactoseh, glucoseh, glucose6phosh,glutamateh, glutamineh, glycerolh, glycineh. glycylglycineh, h2aqh, h2gh, haoh, h202aqh,indolehr lactateh, lactoseh,leucineLh, maltoseh, mannoseh, methanegh, methaneaqh, methanolh,methylamineionh, n2aqh, n2gh, nadoxh, nadpoxh, nadpredh, nadredh, o2aqh. o2gh, pih,ppih, propanol2h, pyruvateh, riboseh, ribose5phosh,ribuloseh, sorboseh, succinateh, sucroseh, trygtophaneLh, ureah, valinelh, xyloseh, xyluloseh); listsgeciesdatah={acetaldehydesp,acetatesp,acetonesp,adenosinesg,adpsg,alaninesp,ammoni asp,ampsp,arabinosesp,asparagineLsp,aspartatesp, atpsp,citratesp,co2gspr co2totsp, coaqsp, cogsp, ethanolsp, ethylacetatesp, formatesp, fructosesp, fumaratesp, galactosesp, glucosesp, g l u c o s e 6 p h o s s g , g l u t a t e s p , glutaminesp, glycerolsp, glycinesp, glycylglycinesp, haaqsp, h2gsp, h2osp, h202aqsp,indolesg, lactatesp, lactosesp,leucineLsp, maltosesp, mannosesp, methanegsp, methaneagsp, methanolsp,methylamineionsp, naaqsp, n2gsp, nadoxsp, nadpoxsp, nadpredsp, nadredsp, o2aqsp, 02gsp,pisp,ppisp, propanol2sp, pyruvatesp, ribosesp, ribose5phossp,ribulosespr sorbosesp, succinatesp, sucrosesp, tryptophanelsp, ureasp, valinelsp, xylosesp, xylulosesp);

Map is used to apply calcdHmat to each of the matrices of species data called up by listspeciesdatah. Clear[acetaldehydeh,acetateh,acetoneh,adenosineh,adph,alanineh,anrmoniah,amph,arabinoseh ,asparagineLh,aspartateh, atph,citrateh,co2gh, coatoth, coaqh, cogh, ethanolh, ethylacetateh, formateh, fructoseh, fumarateh, galactoseh, glucoseh, glucose6phosh,glutamateh, glutamineh, glycerolh, glycineh, glycylglycineh, haaqh, h2gh. haoh, h202aqh,indoleh. lactateh, lactoseh,leucineLh, maltoseh, mannoseh, methanegh, methaneaqh, methanolh,methylamineionh, n2aqh, n2gh, nadoxh, nadpoxh, nadpredh, nadredh, o2aqh, o2gh, pih,ppih, propanolah, pyruvateh, riboseh, ribose5phosh,ribuloseh, sorboseh, succinateh, sucroseh, tryptophaneLh, ureah, valinelh, xyloseh. xyluloseh];

Evaluate[listfnpHish] = Map[calcdHmat, listspeciesdatah];

BasicBiochemData2

215

a 7.0 Calculation of a table of standard transformed enthalpies of

formation of reactants at pH 7 and ionic strengths of 0, 0.10, and 0.25 M listhisreactants={acetaldehydehis,acetatehis,acetonehis.adenosinehis,adghis,a~aninehis, ~niahiS,~phiS,arabinOS~hiS,aSgaraginelhiS,aSQartatehiSr atphis,citratehis,co2ghis, co2tothi6, coaghis, coghis, ethanolhis, ethylacetatehis, formatehis, fructosehis, fumaratehis, galactosehis, glucosehis, glucose6phoshis,glutamatehis, glutminehis, glycerolhis, glycinehis. glycylglycinehis, haaqhis, haghis, haohis, h202aghis,indolehis, lactatehis, lactosehis,leucinelhis. maltosehis, mannosehis, methaneghis, methaneaghis. methanolhis,methylamineionhis, naaghis, nZghis, nadoxhis, nadpoxhis, nadpredhis, nadredhis, oaaghis, 02ghis. pihis,ppihis, propanol2his, pyruvatehis, ribosehis, ribose5~hoshis,ribulose~is, sorbosehis, succinatehis. sucrosehis, tryptophanelhis, ureahis, valinelhis, xylosehis, xylulosehis}; calcdH3I[reactanth~]~=Module[{outl,out2,out3},(*This program calculates the standard transformed enthalpies of formation at 298 K, pH 7, and ionic strengths of 0, 0.10, and 0 . 2 5 M. The reactanth name calls a function of pH and ionic strength or a constant.*) outl=reactanth/.{pH->7,is->O); out2=reactanth/.{pH->7,is->.l}; out3=reactanth/.{pH->7,is->.25}; {outl,out2,out3}l;

Clear[acetaldehydehis,acetatehis,acetonehis,adenosinehis,adphis,alaninehis,ammoniahis,a mghis,arabinosehis,asparagineLhis,aspartatehis, atphis,citratehis,co2ghisr coZtothis, coaghis, coghis, ethanolhis, ethylacetatehis, formatehis, fructosehis, fumaratehis, galactosehis, glucosehis, glucose6phoshis,glutamatehis, glutaminehis, glycerolhis, glycinehis, glycylglycinehis, h2aqhis, haghis, haohis, h202aqhis,indolehis, lactatehis, lactosehis,leucinelhis, maltosehis, mannosehis, methaneghis, methaneaghis, methanolhis,methylamineionhis, naaqhis, naghis, nadoxhis, nadpoxhis, nadpredhis, nadredhis, oaaqhis, olghis, pihis,ppihis, propanol2his, pyruvatehis, ribosehis, ribose5phoshis,ribulose~is, sorbosehis, succinatehis, sucrosehis, tryptophanelhis. ureahis, valinelhis, xylosehis, xylulosehisl;

Map is used to apply calcdH3I to each of the functions for reactants. Evaluate [listhisreactants] = Map[calcdH31, listfnpHish] ;

Table 3 Standard Transformed Enthalpies of Formation (in kJ mol-' ) of Biochemical Reactants at pH 7 and Ionic Strengths of 0, 0.10, and 0.25 M.

216

Mathematica Solutions to Probleius

table3=PaddedF0rmCTableFo~~listhisreactants,TableHeadings->~listreactantsh,{~~I = 0 M","I = 0.10 M","I= 0.25 M")I,TableSpacing->{.3,2)1,{0,2}1

acetaldehyde acetate acetone adenosine adP alanine ammonia arabinose asparagineL aspartate a tP citrate c02g co2tot coaq cog ethano1 ethylacetate formate fructose fumara te galactose glucose glucose6phos glutm a t e glutamine g 1ycero1 glycine glycylglycine h2aq h2g h20 h2 02 aq indole lactate lactose leucineL ma1 tose manno se methaneg me thaneaq methanol methylamineion n2aq n2g nadox nadpox nadpred nadred 02aq

02s

Pl PPi propano12 pyruvat e ribose ribose5phos ribul o s e sorbose succinate sucrose tryptophaneL urea valineL xylose xylulose

I = O M -212.23 -486.01 -221.71 -620.93 -2623.20 -554.80 -132.22 -1633.49 -1043.79 -766.09 -943.41 -3614.23 -1515.78 -393.50 -693.43 -120.96 -110.53 -288.30 -482.00 -425.55 -1259.38 -777.38 -1255.20 -1262.19 -2276.06 -979.89 -805.00 -676.55 -523.00 -734.25 -4.20 0.00 -285.83 -191.17 97.50 -686.64 -2233.08 -643.37 -2238.06 -1258.66 -74.81 -89.04 -245.93 -124.93 -10.54 0.00 0.00 0.00 -29.18 -31.94 -11.70 0.00 -1301.24 -2295.04 -330.83 -596.22 -1034.00 -2037.77 -1023.02 -1263.30 -908.69 -2199.87 -405.20 -317.65 -611.99 -1045.94 -1029.65

1 = 0.10 M

-213.47 -486.63 -223.57 -624.97 -2626.54 -556.97 -133.15 -1637.17 -1046.89 -768.57 -944.96 -3616.65 -1514.14 -393.50 -692.99 -120.96 -110.53 -290.16 -484.48 -425.55 -1263.10 -776.77 -1258.92 -1265.91 -2278.56 -982.06 -808.10 -679.03 -524.55 -736.73 -4.82 -0.62 -286.45 -191.79 95.33 -687.88 -2239.91 -647.40 -2244.89 -1262.38 -76.05 -90.28 -247.17 -126.48 -10.54 0.00 -7.76 -4.96 -32.28 -39.08 -11.70 0.00 -1299.89 -2292.54 -333.31 -596.84 -1037.10 -2041.51 -1026.12 -1267.02 -908.70 -2206.70 -408.92 -318.89 -615.40 -1049.04 -1032,75

I= 0.25 M

-213.87 -486.83 -224.17 -626.27 -2627.24 -557.67 -133.45 -1638.19 -1047.89 -769.37 -945.46 -3616.92 -1513.66 -393.50 -692.86 -120.96 -110.53 -290.76 -485.28 -425.55 -1264.31 -776.57 -1260.13 -1267.12 -2279.30 -982.76 -809.10 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648 . I 1 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1299.36 -2291.57 -334.11 -597.04 -1038.10 -2042.43 -1027.12 -1268.23 -908.70 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

BasicBiochemData2

I8.0

217

Calculation of the standard transformed enthalpies of formation of

reactants at pH 5, 6, 7 , 8, and 9 and ionic strength 0.25 M listhgHreactants={acetaldehydehpH,acetatehpH,acetonehpH,adenosinehpH,adphpH,alaninehpH, ammon~ah~H,amphpH,arab~nosehpH,asparag~neLhpH,aspartatehpH, atphpH,citratehpH,co2ghpH, coatothpH, coaqhpH, coghpa, ethanolhpa, ethylacetatehpH, formatehpli, fructosehpH, fumaratehpa, ga1actosehpI-I. glucosehpli, glucose6phoshpH,glutamatehpH, glutaminehpli, g1ycerolhpI-I. glycinehpli, glycylglycinehpH, h2aghpH. h2ghpH, haohpH, h202aqhpH,indolehgH, lactatehpa, lactosehpH,leucineLhpH, maltosehpli, mannosehpH, methaneghpa, methaneaghpa, methanolhpH,methylamineionhpIi, n2aghpH. nlghpli, nadoxhpH, nadpoxhpH, nadpredhpH, nadredhpa, oaaghpli, 02ghpH, pihpH,ppihpH, propanol2hpH, pyruvatehpa, ribosehpH, ribose5phoshpH,ribulosehpH, sorbosehpH, SuccinatehpH, sucrosehpH, tryptophaneLhpH, ureahpH, valineLhpH, xylosehpH, xylulosehpH); Clear[acetaldehydehpH,acetatehpH,acetonehpH,adenosinehgH,adghpH,alaninehpH,ammoniahpH,a mphpH.arabinosehpH,asparagineLhpH,aspartatehpH, atphpH,citratehpH,co2ghpH, co2tothpH. coaghpli, coghpH, ethanolhpH, ethylacetatehpa, formatehpH, fructosehpH, fumaratehpa, galactosehpH, glucosehpH, glucose6phoshpH,glutamatehpHr glutaminehpa, glycerolhpH, glycinehpH, glycylglycinehpH, h2aghpH, h2ghpH, haohpH, h202aqhpH,indolehpH, lactatehpa, lactosehpH,leucineLhpH, maltosehpH, mannosehpH, methaneghpa, methaneaghpH, methanolhpH,methylamineionhpH, naaghpIi, n2ghpH, nadoxhpa, nadpoxhpH, nadpredhpH, nadredhpH, 02aghpH, 02ghpHr pihpIi,ppihpH, propanol2hpH, pyruvatehpH, ribosehpH, ribose5phoshpH,ribulosehpH, sorbosehpli, succinatehpH, sucrosehpli, tryptophaneLhpH, ureahpH, valineLhpH, xylosehpli, xylulosehpHl ; calcdH5pH[reactanth~]:=Module[{outl,out2,out3,out4,out5},(*This program calculates the standard transformed enthalpies of formation at 298 K, ionic strength 0.25 M and p H s 5, 6, 7, 8, and 9. The reactanth name calls a function of pH and ionic strength or a constant.*) outl=reactanth/.{pH->S,is->.25); out2=reactanth/.{pH->6,is->.25); out3=reactanth/.{pH->7,is->.25>; out4=reactanth/.{pH->8,is->.25); out5=reactanth/.{pH->9,is->.251; {outl,out2,out3,out~,out5)];

Map is used to apply calcdH5pH to each of the functions for the reactants. Evaluate[listhpHreactants] = Map[calcdH5pH, listfnpaish];

’Table 4 Standard Transformed Enthalpies of Formation (in kJ mol-” ) of Biochemical Reactants at I = 0.25 M and pHs of 5, 6, 7, 8, and 9.

218

Mathematica Solutions to Problems table4=PaddedFo~[TableForm[listhpHreactants,TableHeadings-~{listreactantsh,{"~H 51i,11pH6 mi,iigH 7", lipH 8 i * , 1 i p H S1'll,TableSpacing->~.3,2l1, I6,231

acetaldehyde acetate acetone adenosine adP alanine ammonia amp arabinose asparagineL aspartate atP citrate c02g co2tot coaq cog ethanol ethylacetate formate fructose fuma ra te galactose glucose glucose6phos glutamate glutm i n e glycerol glycine glycylglycine h2aq h2g h20 h2 02aq indole lactate lactose leucineL ma1 tose mannose me thaneg me thaneaq methanol methylamineion n2aq n29 nadox nadpox nadpred nadred o2aq 029 Pl

PPi

propano12 pyruva t e ribose ribose5phos ribulose sorbose succinate sucrose tryptophaneL urea valineL xylose xylulose

PH 5 -213.87 -486.96 -224,17 -590.92 -2625.82 -557.67 -133.74 -1635.98 -1047.89 -769.37 -945.46 -3615.67 -1518.50 -393.50 -699.80 -120.96 -110.53 -290.76 -485.28 -425.55 -1264.31 -776.45 -1260.13 -1267.12 -2279.17 -982.76 -809.10 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648.71 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1302.89 -2294.18 -334.11 -597.04 -1038.10 -2034.57 -1027.12 -1268.23 -909.85 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

PH 6 -213.87 -486.85 -224.17 -622.97 -2625.74 -557.67 -133.71 -1636.50 -1047.89 -769.37 -945.46 -3615.43 -1514.96 -393.50 -696.59 -120.96 -110.53 -290.76 -485.28 -425.55 -1264.31 -776.56 -1260.13 -1267.12 -2279.25 -982.76 -809.10 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648.71 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1302.03 -2292.80 -334.11 -597.04 -1038.10 -2038.10 -1027.12 -1268.23 -908.87 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

PH 7 -213.87 -486.83 -224.17 -626.27 -2627.24 -557.67 -133.45 -1638.19 -1047.89 -769.37 -945.46 -3616.92 -1513.66 -393.50 -692.86 -120.96 -110.53 -290.76 -485.28 -425.55 -1264.31 -776.57 -1260.13 -1267.12 -2279.30 -982.76 -809.10 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648.71 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1299.36 -2291.57 -334.11 -597.04 -1038.10 -2042.43 -1027.12 -1268.23 -908.70 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

PH 8

-213.87 -486.83 -224.17 -626.60 -2627.71 -557.67 -130.97 -1638.60 -1047.89 -769.37 -945.46 -3617.49 -1513.49 -393.50 -691.80 -120.96 -110.53 -290.76 -485.28 -425.55 -1264.31 -776.57 -1260.13 -1267.12 -2279.31 -982.76 -809.10 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648.71 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1297.99 -2290.05 -334.11 -597.04 -1038.10 -2043.41 -1027.12 -1268.23 -908.68 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

PH 9 -213.87 -486.83 -224.17 -626.63 -2627.76 -557.67 -115.00 -1638.65 -1047.89 -769.37 -945.46 -3617.56 -1513.47 -393.50 -689.51 -120.96 -110.53 -290.76 -485.28 -4.25.55 -1264.31 -776.57 -1260.13 -1267.12 -2279.31 -982.76 -809.3 0 -679.83 -525.05 -737.53 -5.02 -0.82 -286.65 -191.99 94.63 -688.28 -2242.11 -648.71 -2247.09 -1263.59 -76.45 -90.68 -247.57 -126.98 -10.54 0.00 -10.26 -6.57 -33.28 -41.38 -11.70 0.00 -1297.79 -2287.69 -334.11 -597.04 -1038.10 -2043.52 -1027.12 -1268.23 -908.68 -2208.90 -410.13 -319.29 -616.50 -1050.04 -1033.75

BasicBiochemData2

219

These tables have been given to 0.01 kJ mol-' . In general this overemphasizes the accuracy with which these formation properties are known. However for some reactants for which species are in classical tables, this accuracy is warranted. An error of 0.01 kJ mol-' in the standard transformed Gibbs energy of a reaction at 298 K corresponds with an error of about 1 8 in the value of the apparent equilibrium constant. It is important to understand that the large number of digits in these tables is required because the thermodynamic information is in differences between entries. These tables can be used to calculate changes in standard transformed Gibbs energies of reaction and standard transformed enthalpies of reaction for any biochemical reaction for which all the reactants are in the tables. Standard transfomed entropies of formation and of reaction can also be calculated. The advantage of having this notebook is that these propertiec can be calculated at any desired'pH in the range 5 to 9 and any ionic strength in the range 0 to 0.35 M.

I9.0

w

Examples of calculations using the database on species

9.1 Calculation of pKs of weak acids

When weak acids have pKs in the range between 4 to 10, the standard Gibbs energies of formation at 298.15 K and zero ionic strength of the various species are given in the database on species. In using the program calcpK, it is necessary to give the number associated with the pK. pKs are numbered 1, 2, 3,... from the highest to the lowest in the pH range approximately 4 to 10. calcpK[ speciesmat-, no-, is-] := Module[(lnkzero, sigmanuzsq, lnK),(*Calculates ~ K sfor a weak acid at 298.15 K at specified ionic strengths (is) when the number no of the pK is specified. ~ K sare numbered 1.2, 3,... from the highest pK to the lowest pK, but the highest pK for a weak acid may be omitted if it is outside of the range 5 tO 9. For h3P04, pK1=CalC[piSp,l,{0)] = 7.22.*) lnkzero = (speciesrnat[[no + 1,111 speciesmat~[no,lll)/ (8.31451*0.29815); sigmanuzsq = speciesrnat[[no,311*2 speciesmat[[no + 1,311*2 + 1; 1nK = lnkzero + (1.17582*isA0.5*sigmanuzsg)/ (1 + 1.6*isA0.5); N[-(lnK/Log[lOl ) I 1

-

-

6.46502

calcpK[atpsp,2,.251 3.82652

9.2 Calculation of changes in thermodynamic properties of reactions calctrGerx[ac, pHlist-, islist-] :I Module[{energy}, (*Calculates the standard transformed Gibbs energy of reaction in kJ mol*-l at specified pHs and ionic strengths for a biochemical reaction typed in the form atp+h2o+de:= adp+pi. The names of reactants call the appropriate functions of pH and ionic strength. pHlist and is list can be lists.*) energy = Solve [eq, de] ; energyul, 1, 21 /. pH -pHlist i / . is + islist]

220

Matheniatica Solutions to Problems

This program can be used to calculate standard transformed Gibbs energies of reaction or standard transformed enthalpies of reaction in kJ m o l - l . To calculate the changes in standard transformed enthalpy, an h is appended to the name of the reactant. dGrxatp = calctrGerx[atp+h20 + d e = = adp+pi, { S , 6, 7, 8, 9}, 0.251

{-32.5633, -33.2166, -36.0353, -41.0742, -46.7021) dHrxatp=calctrGerx[atph+h2oh+de==adph+pih,{S, 6, 7, 8 , 9}, 0.251

{-26.386, -25.6892, -23.0327, -21.558, -21.3455}

The corresponding standard transformed entropies of reaction are given by dHrxatp-dGrxatp 0.29815

{20.7188, 25.2473, 43.611, 65.4575, 85.0466)

where these values are in J K-' m o l - I . The standard transformed entropy of reaction increases rapidly above pB 7 because of the production of hydrogen ions. There is an increase in the standard transformed entropy because of the increase in the number of species in the reaction. This program can also be used to produce plots of standard transformed properties of reaction versus pH or ionic strength.

AG' i / (kJ/mol)

-34h

-36 -38. -40.

-42. -44-

9.3 Calculation of apparent equilibrium constants calckprime[eg, pHlist-, islist-] := Module[{energy, dG),(*Calculates the apparent equilibrium constant at specified p H s and ionic strengths for a biochemical reaction typed in the form atp+hao+de==adp+pi. The names of reactants call the appropriate functions of pH and ionic strength. pHlist and is list can be lists.*) energy = Solve [eq, de] ; dG = energy[[l,l,2]] / . pH - > pHlist / . is - > islist; EA(-(dG/(8.31451*0.29815)))l calckprime[atp+h2o+de==adp+gi, 15, 6, 7, 8, 9}, 0.251 6 7 8 {506774., 659585., 2.05626 10 , 1.5698 10 , 1.51989 10 ]

BasicBiochemData2

221

This program can be also used to pepare plots versus pH or ionic strength. Plot [Evaluate[calckprime~atp+h2o+de==adp+p~,pH,O.2511, CpH, 6,8},AxesLabel->{"pH", "K"'l1

i

K'

I

6.5

rn

7

7.5

8 PH

9.4 Calculations of changes in binding of hydrogen ions in biochemical reactions

Biochemical reactions are different from chemical reactions in that they may produce or consume non-integer amounts of hydrogen ions. This is discussed in terms of the change in binding of hydrogen ions af NH in a biochemical reaction, which is given by

A, NH = -(dlogK/dpH) = - (l/ln(lO))(dlnK'/dpH) The change in the binding of hydrogen ions in the hydrolysis of ATP can also be plotted as follows: Plot [Evaluate[ ~1/Log[lO])*D[Log[caIckgrime[atg+h20+de==adp+~~,pH,O.25]],pH]l,~~H,~,9~,~esOrigin> C 5, -1 1, AxesLabel-> C "pH", I \ (N\-H\ ) 1 1 ;

-

-0. -0. -0.

-0.

Since there is a decrease in binding of hydrogen ions in this reaction, hydrogen ions are produced at constant pH.

9.5 Calculation of standard transformed reaction Gibbs energies at other temperatures The program calcdGHT can be used to produce the function of T, pH, and ionic strength that will give the standard transformed Gibbs energies of formation at other temperatures, provided the standard enthalpies of formation of all the species are known.

222

Mathematica Solutions to Problems

calcdGHT[speciesma-1 := Module[{dGzero, dGzeroT, dHzero, zi, nH, gibbscoeff, pHterm, isterm, gpfnsp, dGfn, dHfn),(*This program produces the function of T (in Kelvin), pH, and ionic strength (is) that gives the stndard transformed Gibbs energy of formation of a reactant (sum of species) and the standard transformed enthalpy. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 198.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the transformed Gibbs energies of the species. The output is in the form {dGfn,dHfn), and the energies are expressed in kJ molA-l. The values of the standard transformed Gibbs energy of formation and the standard transformed enthalpy of formation can be calculated at any temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic strength in the range 0 to 0.35 M by use of the assignment operator ( / . ) . * ) {dGzero, dHzero, zi, nH) = Transpose[speciesmat1; gibbscoeff = (9.20483*t)/10A3 - (1.284668*tA2)/10^5+ (4.95199*tA3)/1OA8; dGzeroT = (dGzero*t)/298.15 + dHzero*(l - t/298.15); pHterm = (nH*8.31451*t*Log[10A(-pH)I)/1000; istermG = (gibbscoeff*(ziA2 nH)*isA0.5)/ (1 + 1.6*isA0.5); gpfnsp = dGzeroT - pHterm istermG; dGfn = -((8.31451*t*Log[Plus @@ (EA(-(gpfnsp/((8.31451*t)/1000))))l)/1000~; dHfn = -(tA2*D[dGfn/t, tl); {dGfn, dHfn)]

-

-

Calculate the functions that yield the standard transformed Gibbs energies of the reactants in the reaction atp + h20 = adp + pi at 313.15 K. atp313 = calcdGHT [atpsp]El] /

. t + 313.15;

h20313 = calcdGHT [h2osp]El] / . t + 313.15; adp313 = calcdGHT[adpsp] 111 /. t + 313.15; pi313 = calcdGHT [pisp]El] /. t -+ 313.15;

Calculate the standard transformed reaction Gibbs energies for the hydrolysis of ATP at 313.15 K, pHs 5, 6, 7, 8, and 9 and ionic strengths of 0, 0.10, and 0.25 M. dGerx313 =calctrGerx[atp313+h20313+de==adp313+pi313, {5, 6, 7, 8, 9), {0, 0.1, 0.25}];

TableForm[Transpose[dGerx313], TableHeadings -+ {{"I = 0 MIi, "I = 0.10 Mi*,"1 = 0.25 Mi'}, {"pH 5", l1pH 6 " , "RH 7 " , "pH 8", "RH 9")}1

I = O M

PH 5 -35.9046

PH 6 -36.4816

PH 1 -38.212

PH 8 -43.5265

PH 9 -49.6803

I

0.10 M

-33.6656

-34.2845

-37.1598

-42.482

-48.4002

I = 0.25 M

-32.8611

-33.5895

-36.6852

-42.0518

-41.9136

=

9.6 Calculation of the standard transformed Gibbs energies of formation of the species of a reactant from the apparent equilibrium constant of a reaction To do this all the reactants have to be in the database, except for one or two, The following three programs, which make this calculation in one step, are based on the concept of the inverse Legendre transform. The program to be used depends on the number of species in the reactant. The programs produce entries for the database on species.

BasicBiochemData2

223

calcGeflsplequat-, ~ H c - , ionstr-, 21-, nH1-1 := Module[{energy, trGereactant),(*This program uses CviAfGiIO=-RTlnK' to calculate the standard Gibba energy of formation of the species of a reactant that does not have a pK in the range 4 to 10. The equation is of the form pyruvate+atp-xadp==-8.31451*.29815*Log[K11, where K' is the apparent equilibrium constant at 298.15 K, pHc, and ionic strength is. The reactant has charge number zl and hydrogen atom number nH1. The output is the species vector without the standard enthalpy of formation. * ) energy = Solve[equat, x] / . p H - > pHc / . is - > ionstr; trGereactant = energy[[l,l,Z]l; gefl = trGereactant nH1*8.31451*0.29815*Log[lO]*pHc + (2.91482*(zlA2 nH1)*ionstrA0.5)/ (1 + 1.6*ionstrA0.5); {{gefl, -, zl, nH1})1

-

-

calcGefZsgCequat-, pHc-, ionstr-, 21-, nHl-, pKO-1 := Module[(energy, trGereactant, pKe, trgefpHiS,gefl, gefZ},(*This program uses Evils. fGi'O=-RTlnK' to calculate the standard Gibbs energies of formation of the two species of a reactant for which the pK at zero ionic strength is pKO. The equation is of the form pyruvate+atp-x-adp==-8.31451*.29815*LogIK11, where K' is the apparent equilibrium constant at 298.15 K, pHc, and ionic strength is. The more basic form of the reactant has charge number zl and hydrogen atom number nH1. The output is the species matrix without the standard enthalpies of formation.*) energy = SolveCequat, XI / . pH -> pHc / . is -> ionstr; trGereactant = energyl[l,l,Z]l; pKe = pKO + (0.510651*ionstrA0.5*2*zl)/ (1 + 1.6*ionstrA0.5); trgefpHis = trGereactant + 8.31451*0.29815*Log[l + 10A(pKe pHc)]; gefl = trgefpHis nH1*8.31451*0.29815*Log[lOl*pHc + (2.91482*(zlA2 nH1)*ionstrA0.5)/ (1 + 1.6*ionstrA0.5); gef2 = gefl + 8.31451*0.29815*L0gIlO~~-pK0)1; ({gefl, _,zl, nHl1, Cgef2, _,zl + 1, nH1 + 1111

-

-

calcGef3sp[equat-, pHc-, ionstr-, zl-, nHl-, pKlO-, pK20-1 := Module[{energy, trGereactant, pKe, trgefpHis, gefl, gef2, gef3, pKle, pKZe},(*This program uses xviAfGitO=-RTlnK1to calculate the standard Gibbs energies of formation of the three Species of a reactant for which the pKs at zero ionic strength is pKlO and pK20. The equation is of the form gyruvate+atp-x-adp==-8.31451*.29815*Log[K'], where K' is the apparent equilibrium constant at 298.15 K, ~ H c ,and ionic strength is. The more basic form of the reactant has charge number zl and hydrogen atom number nH1. The output is the species matrix without the standard enthalpies of formation of the three species.*) energy = Solvelequat, x] / . pH -> pHc / . is -> ionstr; trGereactant = energy"l,l,2]1; pKle = pKlO + (0.510651*ionstrA0.5*2*zl~/ (I + 1.6*ionstrA0.5); pK2e = pK20 + (0.510651*ionstrA0.5*(2*zl + 2))/ (1 + 1.6*ionstrA0.5); trgefpHis = trGereactant + 8.31451*0.29815* LOg[l + 10"(pKle pHC) + 10"(pKle + pK2e 2*pHc)l; nH1*8.31451*0.29815*Log[lOl*pHc + gefl = trgefpHis (2.91482*(zlA2 nH1)*ionstrA0.5)/ (1 + 1.6*ionstrA0.5); gef2 = gefl + 8.31451*0.29815*L0g[10"(-pK10)1: gef3 = gef2 + 8.31151*0.29815*L0gClO~~-pK20~1; {{gefl, _, zl, nH1). {gef2, -, zl + 1, nH1 + 11, (gef3, -, zl + 2, nH1 + 2111

-

-

-

The following example is concerned with biochemical reaction EC 1.1.1.37. If the standard Gibbs energies of formation of both coA and acetyl coA are unknown, the convention can be adopted that the standard Gibbs energy of formation of R S - is zero. The standard Gibbs energy of formatin of RSH can be calculated using the pK at zero ionic strength.

224

Mathematica Solutions to rronlems

coA2 = calcdGmat[coA2sp];

Now the data entry for acetylcoA can be calculated from the apparent equilibrium constant (10.8) of this reaction at pH 7.12 and ionic strength 0.05 M. acetylcoAsp2 = CalCGeflSp[ c i t r a t e + c o A 2 + n a d r e d - m a l a t e - x - n a d o x - h 2 0 = =-8.314510.29815Log[10.8],

{{-188.523, -,

7.12, 0.05, 0,

0, 3))

acetylcoA2 = calcdGmat[acetylcoAsp2];

This calculation can be verified by using the data on coA and acetylcoA to calculate the apparent equilibrium constant for this reaction at the experimental conditions. calckprime[malate+acetylcoA2 + n a d o x + h 2 o + d e == citrate+coA2 +nadred, 7.12, 0.051

10.8

m 9.7 Calculation of the thermodynamic properties of a biochemical reaction It is convenient to be able to calculate the standard transformed reaction Gibbs energy, apparent equilibrium constant, and change in binding of hydrogen ions in a biochemical reaction at a series of pHs and ionic strengths. The pH dependencies of the standard transformed reaction Gibbs energies and IS can bt regarded as a consequence of the change in binding of hydrogen ions. calcNHrx[ee, pHlist-, islist-] := Module {energy),(*This program calculates the change in the binding of hydrogen ions in a biochemical reaaction at specified ~ H Sand ionic strengths.*) energy = Solve[eq, del ; D [energy[ [ 1,1,2 1 I , pH]/ (8.31451*0.29815*Log I101 ) / p~ - > pHlist / . is -> islist]

.

rxthermotab[ee, pHlist-, islist-] := Module[{energy, tg, tk, tn), (*This program uses three other programs to make a thermodynamic table of standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the number of hydrogen ions bound in a biochemical reaction.*) tg = calctrGerx[eq, pHlist, islist]; t k = calckprirne[eq, pHlist, islist]; tn = calcNHrx[eq, pHlist, islist]; TableForm[Join[{tg, tk, tn)]]] rxthermotab[pep + adp + de == pyruvate

+ atp, {5, 6, 7, 8, 9), {0, 0.1, 0.25}]

-33.4613 -34.1841 -34.4724

-32.7661 -33.1449 -33.1063

-30.6224 -29.2617 -28.8451

-25.1722 -23.6955 -23.2908

-19.2526 -17.993 -17.5968

728017. 914465.

6 1.09465 10

549974. 640772.

231625. 133784.

25700.8 14166.3

2359.9 1419.79

630867.

113085.

12032.5

1210.04

0.150557 0.0719355 0.0826948

0.151752 0.38045 0.480624

0.700597 0.915575 0.927296

1.06297 0.99698 0.993667

1.01353 0.999809 0.999384

The first row gives the standard transformed reaction Gibbs energies in kJ m o l - l at zero ionic strength, the second row at 0.10 M ionic strength, and the third at 0.25 M ionic strength. The second part of the tsable is made up of apparent equilib-

BasicBiochemData2

225

rium constants, and the third is made up of changes in the binding of hydrogen ions. TableHeadings could be added, but this program allows you to use various numbers of pHs and various numbers of ionic strengths. A vector can be rounded by use of round. round[vec-, params-: ( 4 , 2 1 1 := Flatten[Map[NumberForm[#l, params]

&

,

{vet),

{2111

round[calctrGerx[glucose + atp + de == glucose6phos + adp, { 5 , 6, 7 , 8, 91, 0.251, ( 4 , 211 1-17.41, -19.47, -24.42, -30.11, -35.82)

w

9.8 Printing out biochemical reactions that correspond with a stoichiometric matrix

A biochemical reaction can be represented by a vector of its stoichiometric numbers. A system of biochemical reactions is represented by a stoichiometric number matrix. This stoichiometric number matrix can be used to print out the reactions. The programs that can be used to print out the biochemical reactions are mkeqm and nameMatrix. mketF[c-List,s_List]:=(*c-List is the list of stoichiometric numbers for a reaction. s-List is a list of the names of species or reactants. These names have to be put in quotation marks. * ) Map [Max[#, 0 I &, -cl S->Map[Max[#, 01 &, cl s

.

.

is the transposed stoichiometric number matrix for the system of reactions. s-List is a list of the names of species or reactants. These names have to be put in quotation marks.*)Map[mketF[#,s]&,ml

nameMatrix[m-List,s-Listl:r(*m_List

The first three reactions of glycolysis are ATP + glucose = ADP + G6P G6P = F6P ATP + F6P = ADP + F 16P This system of reactions is represented by the following stoichiometric number matrix.

TableForm [nu] -1 -1

0

1

0

1

0

0

0 -1

1

0

0 -1

u 1 -1 1

226

Mathematica Solutions to Probleins

TableForm[nu, TableHeadings + {names3, {"rx 13", "rx 14",

Glc

rx 13 -1

rx 14

rx 15

ATP

-1

0

-1

G6P

1

-1

0

ADP

1

0

1

F6P

0

1

-1

F16BP

0

0

1

0

"TX

15"}}]

0

mkeqm[{-l, -1, 1, 1, 0, 0}, names31

ATP + GlC -> ADP + G6P nameMatrix[Transpose [nu], names31

{ATP + GlC - > ADP + G6P, G6P -> F6P, ATP + F6P -> ADP + F16BP)

a

9.9 Calculation of standard apparent reduction potentials for half reactions

The standard apparent reduction potential in volts at 298.15 K for a half reaction can be calculated using calcappredpots. As an example of a half reaction consider NAD,, + 2 e - = NADred : calcappredpot [eq-, nu-, pHlist-, islist-] := Module[{energyl,(*Calculates the standard apparent reduction potential of a half reaction at specified p H s and ionic strengths for a biochemical half reaction typed in the form nadox+de==nadred. The names of the reactants call the corresponding functions of pH and ionic strength. nu is the number of electrons involved. pHlist and islist can be lists.*) energy = Solveleq, del ; -(energy~[l,l,2ll/(nu*96.485)) / . pH - > pHlist / . is -> islist]

TableForm[Transpose[calcappredpot[nadox+de == nadred, 2, {5, 6, 7, 8, 9 ) , {0, 0.1, 0.25)]], TableHeadings + { { "I=O MI', " I = O . 10 MI', " I = O . 25 M" } , [ " p H 5", I'pH 6", " p H 7 " , "pH E l 1 , "pH 9"}}, TableSpacing-, {I, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.265275 -0.294855 -0.324435 -0.354015 -0.383595

I=0.10 M

-0.258932 -0.288512 -0.318092 -0.347672 -0.377252

1 ~ 0 . 2 5M

-0.256884 -0.286464 -0.316044 -0.345624 -0.375204

Basii3iochemData2

227

Plot [calcappredpot[nadox+de==nadred,2,pH,.251, {pH,5,9),AxesLabe1->{"pH1',"E' /V"l];

E' / V

-0.2

-0.2

PH -0.3 -0.3 -0.3

9.10 Calculation of equilibrium compositions of a single biochemical reaction or a system of biochemical reactions at specified pH Equilibrium compositions of systems of biochemical reactions can be calculated using the following two programs. The first was written by Fred Krambeck (Mobil Research and Development) and the second was written by Krambeck and Alberty. The Newton-Raphson method is used to iterate to the composition with the lowest possible Gibbs energy or transformed Gibbs energy. equcalcc[as_,lnk_,no_I:=Module[Cl,x,b,ac,m,n,e,k}, ( * as=conservation matrix Ink=-(l/RT)(Gibbs energy of formation vector at T) no=initial composition vector * ) ( *Setup*) {m,n)=Dimensions[asl; b=as .no; ac=as; (*Initialize*) l=LinearSolve[ as.Transpose[asl,-as.(lnk+Log[nl) 1 ; (*Solve*) Do[ e=b-ac.(x=E"(lnk+l.as) ); If[(lO*-lO)>Max[ AbsIel 1, Break11 I; l=l+LinearSolve[ac.Transpose[as*Table~x,~mlll,el, {k, 100) 1 ; If [ k=lOO,Return[i*Algorithm Failed"1 1 ; Return [XI

1

equcalcrx[nt-,lnkr-,no-]:=Module[{as,lnk}, (*nt=transposed stoichiometric number matrix lnkr=ln of equilibrium constants of rxs (vector) no=initial composition vector*) ( *Setup*) lnk=~inearSolve~nt,lnkrl; as="ullSpace [nt1 ; equcalcc[as,lnk,nol

1

The reaction considered here is the hydrolysis of glucose 6-phosphate to glucose and inorganic hosphate at 298.15 K, pH 7, and 0.25 M ionic strength. The objective is to calculate the equilibrium concentrations when the enzyme is added to a 0.10 M solution of glucose 6-phosphate. G6P + H2 0 = Glu + P i This is a single reaction, and so the equilibrium comosition can be readily calculated without a computer program. However,

228

Mathematica Solutions to Problems

it involves an important issue that often arises in enzyme-catalyzed reactions, and that is the problem of water as a reactant in dilute aqueous solutions. The problem is that the activity of water is taken as unity by convention, and so its concentration does not appear in the expression for the apparent equilibrium constant. The conservation matrix at constant pH is G6P H2 0 Glu Pi A = C 6 0 6 0 0 9 1 6 4 P 1 0 0 1 Since the activity of water is taken as unity in dilute aqueous solutions independent of the extent of reaction, the Hz0 column and the oxygen row must be deleted from the conservation matrix: G6P GIU Pi A'= C 6 6 0 P 1 0 1 Therefore the conservation matrix is given by a s = ({6t 6, O}, (1, 0, I}};

The standard transformed Gibbs energies of the reactants at 298.15 K, pH 7, and 0.25 M ionic strength are glucose6ghos / . gH + 7 /. is + 0.25

-1318.92 glucose /. gH -+ 7 /. is + 0.25

-426.708 pi / . pH -+ 7 / . is

+ 0.25

-1059.49 h20 /. g H + 7 /. is + 0.25

-155.658

The standard further transformed Gibbs energies of formation in kJ rno1-l are glucose6phoSft= -1318.92 - 9 (-155.66)

82.02 glucoseft = -426.71

- 6 (-155.66)

507.25 pift = -1059.49

-4

(-155.66)

-436.85

The equilibrium composition is calculated using equcalcc [as,

-

{82.02, 507.25, -436.85) 8.314510.29815

{0.0000919341, 0.0999081, 0.0999081)

I

(0.1, 0, 011

BasicBiochemData2

229

It is more convenient to use equcalcrx because it takes a stoichiometric number matrix and a vector of the apparent equilibrium constants for a set of independent reactions in the system. Note that this program calculates a consevation matrix that is consistent with the stoichiometric number matrix, and uses it in equcalc. The transposed stoichiometric number matrix nt for the reactin without H20 is given by nt = {{-1, 1, 1));

The apparent equilibrium constant is given by calckgrime[glucose6phos+h2o+de == glucose+pi, 7, 0.251

108.375

The equilibrium composition is calculated using equcalcrx[nt, {Log[108.4]), {O.l, 0, 0)]

{0.0000920811, 0.0999079, 0.0999079)

The equilibrium compostion can be verified by calculating the apparent equilibrium constant with the calculated composition EA(nt

. Log[(9.208/10A5,

9.991/10A2, 9.991/10A2)1)

{108.406}

A single enzyme-catalyzed reaction has been used in this example, but a system of reactions can be handled in the same way. The advantage of using matrices and vectors in a computer program is that the same program can be used for large systems of reactions.

Endpackage [ ]

;

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty Copyright 0 2003 John Wiley & Sons, Inc. ISBN 0-471-22851-6

Chapter 1 Apparent Equilibrium Constants 1.1 Plot the fractions ri of ATP in the forms ATP4-, HATP3-, and ATP2-versus pH at 298.15 K and 0.25 M ionic strength. 1.2 Plot the average binding NHof hydrogen ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pH. Show that plotting equation 1.3-13 yields the same result as plotting 1.3-7. 1.3 Plot the average binding NHof hydrogen ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pH at pMg = 2, 3 4, 5 , and 6. 1.4 Plot the average binding &,of pH = 3 4, 5, 6,7, 8, and 9.

magnesium ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pMg at

1.5 Plot the average binding NHof hydrogen ions by ATP at 298.15 K and 0.25 M ionic strength versus pH and pMg. Also plot the rate of change of NHwith pMg for comparison with Problem 1.6 to verify the reciprocity relation. 1.6 Plot the average binding &,of magnesium ions by ATP at 298.15 K and 0.25 M ionic strength versus pH and pMg Also plot the rate of change of NMgWith pH for comparison with Problem 1.5 to verify the reciprocity relation.. 1.7 Plot (a) the base 10 logarithm of the apparent equilibrium constant K and (b) -RTlnK' in kJ mol-'for ATP + H20 = ADP + Piversus pH and pMg at 298.15 K and 0.25 M ionic strength. 1.8 Plot the change in the binding of hydrogen ions A,. N(H+) in ATP + H2 0 = ADP and 0.25 M ionic strength.

+ Pi

versus pH and pMg at 298.15 K

1.9 Plot the change in the binding of magnesium ions A, N(Mg2+)inATP + Hz 0 = ADP + Pi versus pH and pMg at 298.15 K and 0.25 M ionic strength. 1.10 Calculate the acid pKs at 298.15 K and ionic strengths of 0, 0.05, 0.10, 0.15, 0.20, and 0.25 M for all of the acids for which data are given in the table BasicBiochemData.

1.11 Plot the pKs of acetate, ammonia, atp, and pyrophosphate versus ionic strength from I = 0 to I = 0.3 M at 298.15 K. Biochemists are usually only concerned with the pHs in the pH 5 to 9 range. 1.12 (a) Calculate the acid titration curve for ATP at 298.15 K and 0.25 M ionic strength from the binding polynomial P. (b) Integrate the calculated binding curve to obtain In P plus a constant of integration. The needed equations are NH= (-l/ln(lO))(dlnP/dpH) -1n ( 1 0 ) JNHdpH = 1nP + Const 1.13 (a) Test the differentiation of In P to obtain the equation for the binding NH of hydrogen ions by ATP at 298.15 K and ionic strength 0.25 M in the region pH 2 to 10. (b) Test the integration of the equation for NH to obtain the equation for In P. (c) Plot In p versus pH and NH versus pH. The equations involved are NH = [H+]% d[H

j*d[H'

1

= 1nP

+ const

231

232

Mathernatica Solutions to Problems

1.1 Plot the equilibrium mole fractions r, of ATP in the forms ATP4-, HATP3-, and ATP2-versus pH at 298.15 K and 0.25 M ionic strength.

klATP = 3 - 4 3 * 10 " - 7 ; k2ATP = . 0 0 0 1 4 8 ;

Type in the binding polynomial. B = 1 + ( 1 0 " - g H ) / k l A T P + ( 1 0 " ( - 2 * g H ) ) / (klATP*k2ATP) 1 +

10 1.9699 10

6

+

2.91545 10

lo2 pH

1OPH

( l O A - g H ) / ( k l A T P * p ) , ( 1 0 " ( - 2 * g H ) ) / ((klATP*k2ATP) * p ) } , {pH, 3 , 9}, AxesLabel + {"pH", "ri"}];

PlOt[{l/g,

r-

5

4

6

7

8

1.2 Plot the average binding NHof hydrogen ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pH. Show that plotting equation 1.3-13 yields the same result as plotting 1.3-7. klATP = 3 . 4 3 * 10 " - 7 ; k2ATP=0.000148;

n H = ( ( l O A - g H ) / k l A T P + 2 * ( 1 0 A ( - 2 * g H ) ) / (klATP*k2ATP)) / ( 1 + (10"-pH) / k l A T P + ( 1 0 " ( - 2 * g H ) ) / (klATP*kSATP))

3.9398 10lo

6

2.91545 10 1 OPH

lo2 pH 1 I

r ,

10 1.9699 10 2 PH 10

A

2.91545 10

6

1OPH

P l o t [nH, { g H , 3 , 9 3 , AxesLabel

+

{ a m p H " , l l N H t n]};

Apparent Equilibrium Constants

Type in the binding polynomial. P = l + (10”-pH) / k l A T P + 2 * ( 1 0 A ( - 2 * p H ) ) /(klATP*k2ATP)

1 +

3.9398 1 0

10

2 PH 10

6

+

2.91545 10

loPH

Use equation 1.3-7. nHP=-D[LOg[P]r

- I

PHI / L O g [ l O I

10 1 - 2 p H 6 -9.07172 10 2 - 6 . 7 1 3 0 8 10 52 PH PH 10

\

(1

+

3.9398 10lo

lo2

pH

6

2.91545 10 PH 10

)

Log[lOI

\

233

234

Mathematica Solutions to Problems

1.3 Plot the average binding WHofhydrogen ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pH at pMg = 2, 3 4, 5 , and 6. klATP = 3 . 4 3 * 10 " - 7 ; k2ATP= 0 . 0 0 0 1 4 0 ; k3ATP=0.000122; k4ATP=0.0110; k5ATP=O.O279;

The binding polynomial is given by g = 1 + ( 1 0 A - g H ) / k l A T P + ( 1 0 " ( - 2 * p H ) ) / (klATP*k2ATP) + ( 1 0 " - g M g ) / k 3 A T P + ( ( I O A - g H ) * ( l O " - p M g ) ) / (klATP*k4ATP) + (10" ( - 2 * P M g ) ) / (k3ATP*kSATP)

1 +

10 1.9699 10

+

6 2.91545 10

lo2 pH

loPH

8

+ 2.47072 10

-pH 10

-

pMg

293789.

+-+-

8196.72

102 PMg

1 OPMg

The average binding of hydrogen ions is given by nH

= -D[Log[g], pH] /Log[lO] 10 1 - 2 pH -4.53586 10 2 52 P H

(1

1u

+

1.9699 10 lo2 pH

Plot[Evaluate[nH/.

-

6

6.71308 10 1OPH

b

+

2.91545 10 1OPH

+ 2.47072 10

[ p M g + [2, 3, 4, 5, 6 } } ] ,

8

- 5.68905 108 10-pH

-pH - pMg 293789. 10 +-+102 PMg

[pH, 3 , 9}, A x e s L a b e l + [ " p H " ,

-

pMg

8196.72

)

1OPMg llNH"}];

Log[lOl

Apparent Equilibrium Constants

1.4 Plot the average binding pH = 3,4,5, 6,7, 8, and 9.

m~~ of magnesium ions by ATP at 298.15 K and 0.25 M ionic strength as a function of pMg at

k l ATP = 3 . 4 3 * 10 " - 7 i kZATP= O.OOOl48;

k3ATP=0.000122; k4ATP= 0.0118; kSATP= 0 . 0 2 7 9 ;

The binding polynomial is given by B = 1 + ( 1 0 * - p H ) / k l A T P + ( 1 0 " ( - 2 * p H ) ) / (klATP*k2ATP) + ( l O A - p M g ) / k 3 A T P + ( ( l O " - p H ) * (lO"-Mg)) / (klATP*k4ATP) + ( 1 0 " ( - 2 + p M g ) ) / (k3ATPekSATP)

293789. 102

PMg

+-

8196.72

1OPMg

The binding of magnesium ions is given by nMg = - D [ L o g [ p ]

r

235

PMg] / L O g [ l O ]

236

Mathematica Solutions to Problems

18873.6 )

/

1OPM9

((1 +

1.9699 10

10 t

lo2 pH

2.91545 1 0

6 f

1OPH 8

2.47072 1 0

10

-pH

-

pMg

293789.

8196.72

102 PMg

10PMg

+-t-

)

Log[lOI

P l O t [ E v a l u a t e [ n M g /. {pH+ { 3 , 4 , 5 , 6, 7 , 8 , 9 ) } ] , b M g , 2 I 7 } ,A x e s L a b e l + { " p M g " , *INm I' } , P l o t R a n g e + { 0, 1 . 5 ) ] ; NMg

1.41

3

4

5

6

7

1.5 Plot the average binding NH of hydrogen ions by ATP at 298.15 K and 0.25 M ionic strength versus pH and pMg. Also plot the rate of change of WHWith pMg for comparison with Problem 1.6 to verify the reciprocity relation. k l A T P = 3 . 4 3 * 1 0 -7; k2ATP=0.000148; k3ATP=0.000122; k4ATP=0.0118; k5ATP= 0 . 0 2 7 9 ;

The binding polynomial is given by p = 1 + ( 1 0 A -pH) / k l A T P + ( 1 0 ( - 2 *pH)) / (klATP*k2ATP) + ( 1 0 A -pMg) / k3ATP + ( ( l O " - p H ) * ( l O " - p M g ) ) / (klATP*k4ATP) + ( 1 0 " ( - 2 * p M g ) ) / (k3ATP*kSATP)

293789.

2 PMg

10

+-

8196.72 PMg

Apparent Equilibrium Constants

The binding of hydrogen ions is given by nH

-( (

-D[LOg[R]

I

BH] / L O g [ l o ]

1 0 1 - 2 pH 6 -4.53586 10 2 - 6.71308 1 0

52 PH 5.68905 1 0

((1 +

8

10

1.9699 1 0

lo2 pH

2.47072 1 0

nHMg= -D[nH,

8

-PH - PMg)

10

+

10

,

2.91545 1 0

1OPH

-pH - pMg

-

1OPH 6

+ 293789.

+-+-

102 PMg

8196.72 10PMg

)

Log[lOl

PMg] / L O g [ l O ] ;

P l o t 3 D [ n H M g , {RH, 3 , 9 ) , {pMg, 1, 6 } , A x e s L a b b e l + { l l p H i l , "pMg", IIN,,

~ 1 1 i1

237

238

Mathematica Solutions to Problems

1.6 Plot the average binding mM,of magnesium ions by ATP at 298.15 K and 0.25 M ionic strength versus pH and pMg Also plot the rate of change of NMgwith pH for comparison with Problem 1.5 to verify the reciprocity relation. klATP = 3 . 4 3 * 1 0 " - 7 ; k2ATP=0.000148; k3ATP=0.000122; k4ATP= 0.0118; kSATP=0.0219;

The binding polynomial is given by g = l + ( l O A - g H ) / k l A T P + (10" ( - 2 * g H ) ) / (klATP*k2ATP) + ( 1 0 " - g M g ) / k 3 A T P + ((lOA-gH) * ( l O A - p M g ) ) / (klATP*k4ATP) + ( 1 0 " ( - 2 * g M g ) ) / (k3ATP*kSATP)

293789.

+ -8 1 9 6 . 7 2

The binding of magnesium ions is given by

Apparent Equilibrium Constants

18873.6

)

/

loPMg ((1 +

10 1.9699 10 lo2 pH

8 2.47072 10 10

+

6 2.91545 10

1OPH -pH - pMg

+-

+

293789. 102 PMg

+-

8196.72 10PMg

)

LW[lOl)

239

240

Mathematica Solutions to Problems

1.7 Plot (a) the base 10 logarithm of the apparent equilibrium constant K' and (b) -RTlnK' in kJ mol-' for ATP + H 2 0 = ADP

+ Piversus pH and pMg at 298.15 K and 0.25 M ionic strength. klATP = 3.43 * 1 0 " - 7 ; k2ATP= .000140; k3ATP= ,000123; k4ATP= .0118; kSATP= .0279; klADP = 4 . 7 0 * 10 " - 7 ; k2ADP= .000161; k3ADP = .00113; k4ADP= .0431; klP=2.24*10"-7; k2P= -0266; k r e f = .222; pATP = 1 + (10 A - p H ) / klATP + (10 A (-2 * p H ) ) / (k1ATP * k2ATP) + (10 A -pMg) / k3ATP + ( ( l O A - p H ) * (lO"-pMg)) / (klATP*k4ATP) + ( 1 0 " (-2*pMg)) / (k3ATPek5ATP); pADP= 1 +(10"-pH) /k1ADP+ (10" ( - 2 * p H ) ) / (klADP*k2ADP) + ( l O A - p M g ) /k3ADP+ ( ( l O A - p H ) * (10"-pMg)) / (klADP*k4ADP); p P = 1 +(10"-pH) / k l P + ( l O " - p M g ) / k 2 P ; kapp = k r e f * pADP * pP / ( (10 A - p H ) * pATP) ; Plot3D[Log[lO, kappl, { p H , 3, 9}, (pMg, 1, 6}, AxesLabel+ ( " p H " ,

"gMg",

''logK'"}];

Apparent Equilibrium Constants

1.8 Plot the change in the binding of hydrogen ions A, N(H+) in ATP + Hz 0 = ADP and 0.25 M ionic strength.

241

+ Pi versus pH and pMg at 298.15 K

Mathematica Solutions to Problems

klATP = 3 . 4 3 * 1 0 " - 7 ; k2ATP .000140; k3ATP= .000123; k4ATP=.0118; kSATP= .0279; klADP=4.70*10"-7; k2ADP= .000161; k3ADP = - 0 0 1 1 3 ; k4ADP= .0431; k l P = 2.24*10"-7; k 2 P = .0266; k r e € = .222; pATP= 1 +( l O A - p H ) / k l A T P + ( 1 0 " ( - 2 * p H ) ) / (klATP*k2ATP) + ( l O A - p M g ) / k 3 A T P + ( ( 1 0 " - p H ) * ( l O " - p M g ) ) / (klATP*kIATP) + ( 1 0 " ( - 2 * p M g ) ) / (k3ATP*kSATP); pADP= 1 +( l O " - p H ) / k l A D P + ( 1 0 " ( - 2 * p H ) ) / (klADP*k2ADP) + ( l O A - p M g ) /k3ADP+ ( ( l O A - p H ) * ( 1 0 " - p M g ) ) / (klADP*kIADP); p P = 1+ ( 1 0 A - p H ) / k l P + ( 1 0 A -pMg) / k2P; kapp = kref * pADP * p P / ( ( 1 0 - p H ) * pATP) ;

nHrx= - D [ L o g [ k a p p ] , p H ] / L o g [ l O ] ; P l o t 3 D [ n H r x , { p H , 3, 9 } , {pMg, 1, 6 } , A x e s L a b e l + { " p H " ,

"pMg",

"Ar N (If')"}];

1.9 Plot the change in the binding of magnesium ions Ar N(Mg2+)in ATP + H2 0 = ADP + P, versus pH and pMg at 298.15 K and 0.25 M ionic strength.

Apparent Equilibrium Constants

243

klATP = 3 - 4 3 * 1 0 " - 7 ; k2ATP= .000148; k3ATP= .000123; k4ATP= - 0 1 1 8 ; k5ATP = .0279; klADP=4.70*10A-1; k2ADP= .000161; k3ADP= .00113; k4ADP= .0431; k l P = 2.24*10"-7; k 2 P = .0266; k r e € = -222; pATP= 1 + ( l O A - p H ) / k l A T P + ( 1 0 " ( - 2 * p H ) ) / (klATP*kSATP) + ( l O A - p M g ) / k 3 A T P + ( ( l O A - g H ) * ( l O A - g M g ) ) / (klATP*k4ATP) + ( 1 0 " ( - 2 * g M g ) ) / (k3ATP*kSATP); pADP= 1 +( l O A - g H ) / k l A D P + ( 1 0 " ( - 2 * p H ) ) / (klADP*kZADP) + (1O"-gMg) /k3ADP+ ( ( 1 0 " - p H ) * ( l O A - p M g ) ) / (klADP*k4ADP); p P = 1+ ( 1 0 " - p H ) / k l P + ( 1 0 " - g M g ) / k2P; kapp = kref * PADP * p P / ( (10" -BH)* pATP) ;

nMgrx= - D [ L o g [ k a p p ] , pMg] / L o g [ l o ] ; Plot3D[nMgrx, { g H , 3, g } , {pMg, 1, 61, A x e s L a b e l

-)

{ l l g H 1 m ,"pMg",

"Az N ( M g * ' )

"}I;

1.10 Calculate the acid pKs at 298.15 K and ionic strengths of 0, 0.05, 0.10, 0.15, 0.20, and 0.25 M for all the acids for which data are given in the package BasicBiochemData2.

(BasicBiochemData2 needs to be loaded.)

244

Matheinatica Solutions to Problems

CalCpK[SpeCieSmat-, no-, is-] := Module [ {lnkzero, sigmanuzsg, InK) , (*Calculates pKa for a weak acid at 298.15 K at specified ionic strengths (is)when the number no of the pK is specified. pKs are numbered 1, 2, 3,. ..from the highest pK to the lowest pK, but the highest pK for a weak acid may be omitted if it is outside of the physiological range p H 5 to 9. For H3P04, gK1=CalCgK[giSp,l,(O}] = 7.22*) lnkzero = (speciesmat[ [no + 1, 13 ] speciesmat [ [no, 11 ]) / (8.31451 * .29815); sigmanuzsg = speciesmat [ [no, 31 ] A 2 speciesmat [ [no + 1, 31 ] A 2 + 1; lnK=lnkzero+ (1.17582*isA .5) *sigmanuzsg/ (1+1.6*isA.5); N [ 1nK / Log [ 101 ]

-

1

-

-

As a check on this program, pKl(I=O) for ATP is 7.60. sigmanusq is 16+1-9=8. pK1(1=0.25) can be calculated outside the program using -(Log[1OA-7.6O1+(1.17582*isA.5)*8/(l+l.6*isA.5~~/Log~lOl/.is-~.25 6.46522

names = { "acetatepKl", 'lacetylphospK1",n1acetylphospK211, "adeninepKl", "adenosinepK1", "adppKl", "adppK2". "ammoniapK1ml,lmamppK1l*, 11amppK21*, "atppK1". 1EatppK21r, "bpgpK1". "CitrateRKl", "citratepKZ", "citrateisopKl", 11citrateisopK2","carbondioxidepKl", 11carbondioxidepK2","coApK1 n , "cysteineLpK1n , "dihydroxyacetonephospK1", " f ructose6pho~pKl"~ " fructosel6phospK1", "fructosel6phospK2 I - , "fumaratepK1' I , '1fumaratepK211, "galactoselphospKl", "glucose6phospK1", l'glucoselphospK1i~, ~1glycero13phospK1~~, "glutathioneredpK1' I , 'gglyceraldehydephospKl~l, "malatepKl', lloxalatepK1lm, "phosphoeno1pyruvateKl1', 1~phosphoglycerate2pKl'1, "~hos~hoglycerate3~K1", "phosphatepKlml,"gyrophosghategK1". mmpyrophosphatepK2't, "~yrophosphatepK3"~ "riboselphospKl", "ribose5ghospKln, llsuccinatepK1ls, "succinatepK2", "succinylcoApK1ll,"thioredoxinredpKl", v1thioredoxinredpK2q1) ; acetatepK1 = NUmberForm[calcpK[acetatesp, 1, (0, .05, .l, .15, -2, .25}], 31 ;

a d e n o s i n e p K l = ~ e r F o r m [ c a l c p K [ a d e n o s i n e s p1, , {O, -05, .1, .15, .2, .25)], 31; adppKl = NunberForm[calcpK[adpsp, 1, {O, -05, .I, .15, .2, .25}], 31 2 adppK2 =NumberForm[calcpK[adgsp, 2, {O, .05, .1, .15, .2, .25}], 31; aImOniapK1 = NumberForm[calcpK[ammoniasp, 1, (0, .05, .1, .15, .2, .25}], 31; amppKl =NbmberForm[calcpK[ampsp, 1, {O, .05, -1, .15, .2, .25}], 31; dlIlppK2 = NumberForm[calcpK[ampsp, 2,

{o,

.05,

atPpK1 = NumberForm[calcpK[atpsp, 1,

{o,

.05, .1, .IS, .2, .25)], 31 ;

.I, .15, .2, .25}], 31;

atppK21 NumberForm[calcpK[atpsp, 2, {0, .05, .l, .15, .2, .25}], 31 ;

245

Apparent Equilibrium Constants citratepKl = NunberForm[calcpK[citratesp, 1, {O, .05, .l, .15, .2, .25}], 31; citratepK2 cINunberForm[calcpK[citratesp, 2, (0, .05, .l, -15, .2, .25}], 31 ; citrateisopKI= NumberFonn[calcpK[citrateisosp, 1, { O , .05, .1, .15, -2, .25}], 31 ; citrateisopK2 = NumberForm[calcpK[citratesp, 2, {0, .05, -1, -15, -2, .25}], 31 ; carbondioxidepKl= ~ e r F o r m [ c a l c p K [ c o 2 t o t s p ,1, { O , .05, .l, .15, .2, .25}], 31; carbondioxidepK2 = NunberForm[calcpK[co2totsp, 2, (0, .05, -1, .15, .2, .25}], 31 ;

coA~K1=NumberForm~calc~K~coAsp,l,{0,.05,.1..15,.2,.25~1,31;

cysteineLpKl=NumberForm[calcpK[cysteineLsp, 1, (0, .05, .l, .15, .2, .25)], 31; d~hydroxyacetonephos~Kl=~erForm~calcpK~dihydroxyacetone~hoss~,1,{O,.O5,.1,.15,.2,.25 31,31; fructose6phosgK1=NumberForm[calcpK[fructose6phossp, 1, {0, .05, .l, .15, -2, .25}], 31; fructosel6phospK1=herForm[ca1c~KCfructose16~hossg,1,~0,.05,.1,.15,.2,.25~1,31; fructosel6phospK2=NumberForm[calcgKCfructosel6~hossp,2,{Or.O5,.1,.15,.2,.25}],3~;

fwarate~K~=NumberForm~calcpK[fumaratesp,l,{0,.05,.1,.15,.2,.25}1,31; fumaratepK2=~erForm~calc~K~fumaratesg,2,{0,.05,.l,.15,.2,.25~1,31; galactoselphospK1

NumberForm[calcgK[galactose1phosspr 1, (0, . 0 5 , .1, .15, .2, .25}], 31 ;

glucose6phospKl = NunberForm[calcpK[glucose6phossp, 1, (0, .05, .l, .15, .2, .25

1,

31;

glucoselphospK1 = NumberForm[calcpK[glucoselphossg, 1, (0, . 0 5 , .l, .15. .2, .25

1,

31;

glutathioneredpKl=NumberForm[calcpK[glutathioneredsp, 1, {O, .05, .l, .15, .2, .25}], 31; glyceraldehydephospK1=NumberForm[calcpK[glyceraldehydeghossg,1,{O,.O5,.1,.15,.2,.25~1,3

I;

glycerol3phospK1=NumberForm[:calc~K[glycerol3phossp,1,{O,.O5,.1,.15,.2,.25}1,31; malatepK1

NumberForm[calcpK[malatesp, 1, {O, .05, .1, .15, .2, .25}], 31;

oxalatepKl= NurnberForm[calcpK[oxalatesp, 1, {0, .05, .l, .15, .2, .25}], 31 ;

~hosphoenolpyruvatepK1=~erForm[calcpK[peps~,l,{O,.05,.l,.15,.2,.25)1,31;

~hosphoglycerate2pK1=~erForm~calcpK[pg2sp,1,{O,.O5,.1,.15,.2,.25~1,31; phosphoglycerate3pK1=NumberForm[calcpK[pg3s~,1,CO,.O5,.1,.15,.2,.25~1,31;

phosphatepK1 = NumberForm[calcpK[pisp, 1, {O, .05, .l, .15, .2, .25)], 31 ; pyrophosphatepKlm NmberForm[calcpK[ppisp, 1, {O, .05, .l, .15, .2, .25)], 31; pyrophosphatepK2 = ~ e r F o ~ [ c a l c p K [ p p i s p2, , {O, .05, -1, .15, .2. .25)] I 31; pyrophosphatepK3m NmberForm[calcpK[ppisp, 3, {O, .05, .l, .15, .2, .25}], 31 ;

246

Mathematica Solutions to Problems

riboselphospK1 = NumberForm[calcpK[riboselphossp, 1, {0, .05, .l, -15, -2, .25}], 31; ribose5phospKl = ~erForm[calcpK[ribose5phossp,1, {0, .05, .1, .15, .2, .25}], 31;

thioredoxinredgKl=NumberForm[calcgK[thioredoxinredsp, 1, {O, .05, -1, .15, .2, .25}], 3 1 ; thioredoxinredgK2 =NumberForm[calcpK[thioredoxinredsp, 2, {0, .05, .l, .15, -2, .25}], 31; TableForm[{acetatepKl, acetylphospK1, acetylphospK2, adeninepK1, adenosinepK1, adppK1, adppK2, ammoniapK1, mppKl, amppK2, atppK1, atppK2, bpgpKl, citratepK1, citratepK2, citrateisopK1, citrateisopK2, carbondioxidepK1, carbondioxidepK2, coApK1, cysteineLpK1, dihydroxyacetonephospK1, fructose6phospK1, fructosel6phospK1, fructosel6phospK2, fumaratepK1. fumarategK2, galactoselphospK1, glucose6ghospK1, glucoselphospK1, glutathioneredpK1, glyceraldehydephospK1, glycerol3phospK1, I'nahitepKl, oxalatepK1, phosphoenolpyruvatepK1, phosphoglycerate2pK1, phosphoglycerate3pK1, phosphatepK1, pyrophosphatepK1, pyrophosphatepK2, pyrophosphatepK3, riboselphospK1, ribose5phospK1, succinatepK1, succinatepK2, succiny~coApKl,thioredoxinredpK1, thioredoxinredpK2}, 1sI=0.051i, ilI=O.lO1i, "I=0.15i1,"I=O .20", 1iI=0.25r1)}] TableHeadings + {names. {'lI=Omi.

acetatepKl

1=0 I=O.O5 I=O.10 I=O.15 I=0.20 I4.75, 4.59, 4.54, 4.51, 4.49, 4.47)

acetylphospK1

18.69, 8.35, 8.26, 8.2, 8.16, 8.12)

acetylphospK2

I5.11, 4.94, 4.9, 4.87, 4.85, 4.83)

adeninepK1

{4.2, 4.2, 4.2, 4.2, 4.2, 4.2)

adenosinepK1

I3.47, 3.47, 3.47, 3.47, 3.47, 3.47)

adppKl

17.18, 6.67, 6.53, 6.44, 6.38, 6.33)

adppK2

14.36, 4.02, 3.93, 3.87, 3.83, 3.79)

ammoniapKl

19.25, 9.25, 9.25, 9.25, 9.25, 9.25)

amppK1

I6.73, 6.39, 6.3, 6.24, 6.2, 6.16)

amPPK2

I3.99, 3.82, 3.77, 3.74, 3.72, 3.71)

atppK1

I7.6, 6.93, 6.74, 6.62, 6.53, 6.47)

atppK2

(4.68, 4.17, 4.03, 3.94, 3.88, 3.83)

bPgPK1

I7.96, 7.29, 7.1, 6.98, 6.9, 6.831

citratepK1

I6.39, 5.89, 5.75, 5.66, 5.59, 5.54)

citratepK2

I4.76, 4.42, 4.33, 4.27, 4.22, 4.19}

CitrateisopKl

16.4, 5.9, 5.76, 5.67, 5.6, 5.55)

citrateisopK2

14.76, 4.42, 4.33, 4.27, 4.22, 4.19)

carbondioxidepK1

{10.3, 9.99, 9.9, 9.84, 9.8, 9.76}

carbondioxidepK2

16.37, 6.2, 6.15, 6.12, 6.1, 6.08)

coApKl

18.38, 8.21, 8.16, 8.14, 8.11, 8.1)

I=O.25

Apparent Equilibrium Constants CysteineLpKl

I8.38, 8.21, 8.16, 8.13, 8.11, 8.09)

dihydroxyacetonephospK1

15.7, 5.36, 5.27, 5.21, 5.17, 5.13)

fructose6phospKl

I6.27, 5.94, 5.84, 5.78, 5.74, 5.7)

fructosel6phospKl

I6.65, 5.98, 5.79, 5.67, 5.59, 5.521

fructosel6phospK2

(6.05, 5.54, 5.41, 5.32, 5.25, 5.2)

fumaratepK1

I4.6, 4.27, 4.17, 4.11, 4.07, 4.03)

fumaratepK2

{3.09, 2.93, 2.88, 2.85, 2.83, 2.81)

galactoselphospK1

I6.15, 5.81, 5.72, 5.66, 5.61, 5.58)

glucose6phospKl

(6.42, 6.08, 5.99, 5.93, 5.89, 5.85)

glucoselphospK1

I6.5, 6.16, 6.07, 6.01, 5.97, 5.93)

glutathioneredpK1

I8.34, 8., 7.91, 7.85, 7.81, 7.77)

glyceraldehydephospK1

{5.7, 5.36, 5.27, 5.21, 5.17, 5.13)

glycerol3phospKl

I6.67, 6.33, 6.24, 6.18, 6.14, 6.1)

ma latepKl

{5.26, 4.92, 4.83, 4.77, 4.73, 4.69)

oxalatepK1

C4.28, 3.94, 3.85, 3.79, 3.75, 3.71)

phosphoenolpyruvateK1

{7., 6.5, 6.36, 6.27, 6.2, 6.151

phosphoglycerate2pKl

I7.64, 7.14, 7., 6.91, 6.84, 6.79)

phosphoglycerate3pKl

I7.53, 7.03, 6.89, 6.8, 6.73, 6.68)

phosphatepK1

I7.22, 6.88, 6.79, 6.73, 6.69, 6.65)

pyrophosphatepK1

(9.46, 8.79, 8.6, 8.48, 8.4, 8.33)

pyrophosphatepK2

(6.72, 6.21, 6.08, 5.99, 5.92, 5.871

pyrophosphatepK3

I2.26, 1.92, 1.83, 1.77, 1.73, 1.69)

riboselphospK1

I6.69, 6.35, 6.26, 6.2, 6.16, 6.12)

ribose5phospKl

I6.69, 6.35, 6.26, 6.2, 6.16, 6.12)

succinatepK1

I5.64, 5.3, 5.21, 5.15, 5.11, 5.071

succinatepK2

I4.21, 4.04, 3.99, 3.96, 3.94, 3.92)

succinylcoApK1

{4.21, 4.04, 4., 3.97, 3.95, 3.93)

thioredoxinredpK1

I8.64, 8.3, 8.21, 8.15, 8.11, 8.071

thioredoxinredpK2

I8.05, 7.88, 7.83, 7.8, 7.78, 7.76)

247

1.1 1 Plot the pKs of acetate, ammonia, atp, and pyrophosphate versus ionic strength from I = 0 to I = 0.3 M at 298.15 K. Biochemists are usually only concerned with the pHs in the pH 5 to 9 range .

(BasicBiochemData2 needs to be loaded)

248

Matheniatica Solutions to Problems

CalCpK[SpeCieSmat-, no-, is-] := Module[{lnkzero, sigmanuzsg, InK), (*Calculates pKa for a weak acid at 298.15 K at specified ionic strengths (is)when the number no of the pK is specified. ~ K are s numbered 1, 2, 3,...frcrm the highest pK to the lowest pK, but the highest pK for a weak acid may be omitted if it is outside of the physiological range pH 5 to 9. For H3P04, gK1=CalCpK[giSp,l,{O}] = 7 . 2 2 * ) lnkzero= (speciesmat[ [no+l, 113 -speciesmat[[no, 133) / (8.31451e.29815); sigrnanuzsq = speciesmat [ [no, 31 ] A 2 speciesmat [ [no + 1, 31 ] A 2 + 1; 1nK = lnkzero + (1.17582 *is A .5) * sigmanuzsg/ (1 + 1.6 *is A .5); N [ - 1nK / Log [ 101 ]

-

1

plotacetate-Plot [acetatepKl,Cis, 0 , . 3 1 ,Axesorigin->(0,4.45} ,AxesLabel-> { "I/M", "pK"} 1 ;

0.05

0.1

0.15

0.2

0.25

0.3

I/M

249

Apparent Equilibrium Constants

PK

17.51

15i 12.5

c

1,.

,

.

I

.

0.05

,

,

,

I

.

0.1

.

.

,

,

.

0.15

,

.

.

I

,

0.2

,

,

.

I

,

0.25

,

,

,

,

0.3

I,M

atppKl = calcpK[atpsp, 1, is] ; glotatpl=Plot [atppKl,{is, 0, . 3 } ,Axesorigin->{ 0 , 6 . 4 1, AxesLabel-> { " I / M "

," \ !\ ( p K \ - l \

)

" 11 ;

atppK2 = CalCpK[atpSp, 2, is] ; glotatp2=Plot latppK2, {is, 0, . 3 1,Axesorigin->{ 0,3.8) ,AxesLabel->{ "I/M", " \ !\ ( g K \ - 2 \

I'

11 ;

250

Mathematica Solutions to Problems

pyrophosphatepK1 = calcpK[pgisp, 1, is] ;

glotgyrol=Plotlpyrophos~hatepKl,{is,O,.3},~esOrigin-~{O,8.2~,~e~Label> { l l I / M n , 'I \ ! \ (pK\-1\) '' 1I ;

0.05

0.1

0.15

0.2

0.25

'

0.3

I/M

pyrophosphatepK2 = calcpK[ppisp, 2, is] ; ~lotpyro2=P~ot[pyrophosphatepK2,{is,O,.3},~esOrigin-~CO,5.8~,~e~Label> { B I I / M 1 s , " \ ! \ (pK\-2\)" 1I ;

Apparent Equilibrium Constants

251

F

1.12 (a) Calculate the acid titration curve for ATP at 298.15 K and 0.25 M ionic strength from the binding polynomial P. (b) lntegrate the calculated binding curve to obtain In P plus a constant of integration. The needed equations are NH= (-l/ln(lO))(dlnP/dpH) -In ( 1 0 ) INHdpH= InP + const

(a) The titration curve can be calculated by differentiating the logarithm of the binding potential P. ~~1+(10"-~H)/(10*-6.47)+((1OA~~H)"2)/((1OA~6~47)*~~OA~3~83~~

1 I

r

1.99526 1 0

8

10

2 PH

10 +

2.95121 10

1OPH

6

252

Mathernatica Solutions to Problems plot [p, {pH, 2,lO 1, AxesLabel-> C"pH", "p")I ;

P

10 1 -4.59426 10 2

(1 +

1.99526 lo1" 2 PH 10

plot [nH,{ pH, 2,lO

-

2 pH

6 6.79541 10

2.95121 l o u 1 OPH

} Axes Label

,

-

- > { "pH

)

Log[lol

, \ !\ ( N\-H\

)

'I

1I ;

Apparcnt Equilibrium Constants

253

(b) Integration of the binding curve gives 1nP plus a constant. lngcalc=-Log [lo]*Integrate [nH,pHl - 4 . 6 0 5 1 7 pH

+ 1. L o g [ 6 7 7 6 . 3 9 + l o P H ] + 1. L 0 g C 2 . 9 4 4 4 3 l o 6 + l o p H ]

(lnpcalc-Log[pl)/.pH->E5,6,7) {O.,

3.55271 1 0

-15

, 7.10543 1 0

-15

1

Thus the integration constant is zero within machine accuracy. Plot [lnpcalc,(pH,2,10),AxesLabel->C"pH","ln

p")];

In P

1.13 (a) Test the differentiation of In P to obtain the equation for the binding NH of hydrogen ions by ATP at 298.15 K and ionic strength 0.25 M in the region pH 2 to 10. (b) Test the integration of the equation for NH to obtain the equation for In P. (c) Plot In p versus pH and NH versus pH. The equations involved are

254

Mathematica Solutions to Problems

(a) First we express the binding potential P as a function of the hydrogen ion concentration, represented by h. ~=l+h/10"-6.47+h"2/((lOA-6.47)*(1OA~3.83))

6 1 + 2.95121 10 h

i

10

1.99526 10

h

2

Plot[g, {h,10A-2,10A-10},AxesLabel->i11h~',"p11~l;

P

Plot [Log[p] ,{h, 1 0 A - 2 , 1OA-1O),Axe~Label->{~'h", "In g " 3 1 ;

In P

0.002

0.004

0.006

0.008

'

0.01

The equation for the titration curve is obtained by use of the following differentiation: nH=h*D[Log[ P I , hl

h

Apparent Equilibrium Constants

255

10 h (2.95121 lo6 + 3.99052 10 h) 6 10 h2 1 + 2.95121 10 h + 1.99526 10

(b) This equation can be integrated to obtain lnp: Integratel(nH/h),hl -7 1. Log[3.39624 10 + hl + 1. Log[0.000147571 + hl

This should be lnp, which is

6 10 2 h ] Log[l + 2.95121 10 h + 1.99526 10

except for an integration constant. We can compare the two expressions for In p by calculating numerical values at pH 2,2.5, 3, 3.5, ...10: ph=Table[n,{n,2,10,.5}] I2, 2.5, 3., 3.5, 4., 4.5, 5., 5.5, 6., 6.5, 7., 7.5, 8., 8.5, 9., 9.5, 10.1

1 100

I-,

-6 0.00316228, 0.001, 0.000316228, 0.0001, 0.0000316228, 0.00001, 3.16228 10 , 1. 1(

3.16228

1.

3.16228

1.

3.16228 lo-’,

-10 1. lo-’, 3.16228 10 , 1.

LOg[p]/.h->hh I14.521, 12.2494, 10.0391, 7.98259, 6.20586, 4.73863, 3.48147, 2.35442, 1.37906, 0.6602: 0.0892422, 0.0290869, 0.00928946, 0.00294688, 0.000932821, 0.000295078}

These are the values of In p calculated from pK1 and pK2. Integrate[(nH/h),hl/.h->hh {-9.19566, -11.4672, -13.6775, -15.734, -17.5108, -18.978, -20.2352, -21.3622, -22.3376, -23.4579, -23.6274, -23.6875, -23.7073, -23.7137, -23.7157, -23.7163)

These are the values of In p calculated by integration of the binding curve (that is, nH versus h) (Integrate[(nH/h),hI/.h->hh)-(Log[pl /.h->hh) {-23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.711 -23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.7166, -23.7166)

This is the integration constant. Now calculate values of p at 0.5 pHs.

6 {2.02472 10 , 208854., 22904.2, 2929.44, 495.634, 114.275, 32.5065, 10.5318, 3.97106, 1. 1.29529, 1.09332, 1.02949, 1.00931, 1.00292, 1.00091, 1.00027)

256

Mathematica Solutions to Problems

This can be compared with the values calculated directly from In p: p/.h->hh 6

I2.02478 10 , 208860., 22904.8, 2929.52, 495.647, 114.278, 32.5074, 10.5321, 3.97116, 1 1.29532, 1.09335, 1.02951, 1.00933, 1.00295, 1.00093, 1.0003}

The agreement is quite good as expected. We can also plot the value of P calculated by the successive differentiation and integration to see whether it is the same as the plot in part b. Plot [Evaluate[Exp[Integrate[(nH/h) , h ] + 2 3 . 7 1 6 6 1 1 , ~h,10A-2,10A-10},AxesLabel->I"h"r"g")l;

P 2X1O6

-

1.5 x 1 0 6 -

1x106-

500000 -

0.002

0.004

0.006

0.008

'

0.01

h

(c) If we introduce the relation between h and pH, the expressions for p and nH will be converted to functions of pH.

10-pH

B 1 +

10 1.99526 10

2 PH 10

6

+

2.95121 10 PH 10

Apparent Equilibrium Constants

Since the computer will substitute h=lOA-pH,we obtain the equation for the binding cuve by simply typing nH. nH

10 6 3.99052 10 2.95121 10 + 1OPH 10 6 1.99526 10 2.95121 10 loPH ( 1 + + ) lo2 pH 1 OPH Plot [ nH, {gH, 2,lO } ,AxesLabel - > { "gH", 'I \ ! \ (N\-H\ ) 'I 1 I

;

257

258

Mathematica Solutions to Problems

Chapter 3 Chemical Equilibrium in One Phase Systems 3.1 Use the table of basic data to calculate the acid dissociation constants of ATP, ADP, and Pi and the equilibrium constant for the reference reaction ATP4- + H 2 0 = ADP3- + HPO4'-+ H+ at 298.15 K and ionic strengths of 0, 05, 0.10, 0.15, 0.20, and 0.25 M. 3.2 For the solution reaction A = B, assume that the standard Gibbs energy of formation of A is 20 kJ mol-' and of B is 18 kJ mol-' at 298.15 K. (a) For a reaction starting with a mole of A at a concentration of 1 M, plot the Gibbs energy of the mixture versus extent of reaction from zero to unity and identify the approximate extent of reaction at equilibrium. (b) Identify the equilibrium extent of reaction more precisely by plotting the derivative of the Gibbs energy of the mixture with respect to extent of reaction. (c) Calculate the equilibrium constant and verify the equilibrium extent of reaction. 3.3 Calculate the standard Gibbs energy changes and equilibrium constants in terms of species for the following reactions at 298.15 K and ionic strengths of 0, 0.10, and 0.25 M. Summarize the calculations in two tables. NAD- + H2(g) = NADH2- + Hf (a) NADP3- + Hz(g) = NADPH4- + H+ (b) NAD- + NADPH4-= NADH2- + NADP3(c) CH3 CHIOH + NAD- = CH3 CHO + NADH2- + H+ (d) CH3 CHO + NAD- + H 2 0 = CH3 C 0 2 - + NADH'- + 2 H+ (e) (0 C3 H7 NO2 + NAD- + H 2 0 = C3 H3 0-+NADH2- + N&+ + H+ The last reaction involves L-alanine and pyruvate. 3.4 Plot the acid dissociation constant of acetic acid from 0 OC to 50 "C given that at 298.15 K, Af Co = 27.14 kJ mol-', A, H" = -0.39 kJ mol-', and A, C,"= -155 J K-' mol-". Assume zero ionic strength. 3.5 (a) Calculate the function of T that gives the values of the Debye-Huckel constant a at the temperatures in Table 3.1 in Section 3.7. Plot the data and the function. (b) Calculate the function of T for RTa. (c) Calculate the function of T for RT2(da/aT)p. (d) Use these functions to calculate these coefficients at 0, 10,20,25, 30, and 40 O C .

3.6 Calculate the standard Gibbs energies of formation of the three species of ATP at temperatures of 283.15 K, 298.15 K, 298.15 K and ionic strengths of 0,O. 10, and 0.25 M. 3.7 Calculate the adjustments to be subtracted from pH, obtained with a pH meter to obtain pH,= -log[H+ at 0 "C to 40 "C and ionic strengths of 0, 0.10, and 0.25 M. 3.8 Calculate the standard enthalpies of formation of the three species of ATP at 283.15 K, 298.15 K, and 313.15 K at ionic strengths of 0, 0.10, and 0.25 M 3.9 There are two ways to obtain values for the enthalpy coefficient in equation 3.6-5 as a function of temperature: (a) Calculate the derivative with respect to T of the Gibbs energy coefficient divided by T. (b) Fit the enthalpy coefficients of Clarke and Glew to AT2+ BT3. Use both of these methods and make plots to compare these functions with the values in Table 3.1 3.10 Plot the activity coefficients of ions with charges I, 2, 3, and 4 versus the ionic strength at 0 "C. Repeat these calculations at 25 "C and 40 "C

260

Matheinatica Solutions to Problems

3.1 Use the table of basic data to calculate the acid dissociation constants of ATP, ADP, and Pi and the equilibrium constant for the reference reaction ATP4- + H 2 0 = ADP3- + HP04’-+ H+ at 298.15 K and ionic strengths of 0 , 05, 0.10, 0.15, 0.20, and 0.25 M.

(BasicBiochemData2 has to be loaded) The following program calculate the function of ionic strength that gives the standard Gibbs energy of formation of a species. calcdGis [species-] := Module[ {dGzero, zi, isterm}, (*This program calculates the function of ionic strength (is) that gives the standard Gibbs energy of formation of a species at298.15 K. The input is a list for the species that gives the standard Gibbs energy of formation, the standard enthalpy of fonnation,the electric charge, and the number of hydrogen atoms in the species. Energies are expressed in kJ molA-l.*) dGzero= species[[l]]; z i = species[[3]]; isterrn=2.91482*(ziA2)*(isA.5)/ (1+1.6*isA.5); dGzero - isterm]

The basic data on the hydrogen ion species is hydroionsp=EO,O,l,lI

hydroion=calcdGis[hydroionspl -2.91482 is

0.5

0.5

1 + 1.6 is

Now we need to produce a list for each species from the entries in BasicBiochemData2. atpH0=calcdGis~atpsp~~1111 0.5

-2768.1 -

46.6371 is 0.5 1 + 1.6 is

atgHl=calCdGiS[atgSg[[2]]];

atpHZ=calcdGis [atpsp[ 131 1 1 ; adpH0=calcdGis~adpsp[[llll;

adpHl=calcdGis~adpsp~[2]11; adgH2=calcdGis[adpsp[[31]1; ghosphateH1=calcdGis[pisp[[lllI; phosphateH2=calcdGis[pisp[[21]1;

h2o=calcdGis lh20sp C 111 1 1 ;

Chemical Equilibrium in One Phase Systems

261

calckrx[eq_,islist~l:=Module[{ener~,dG},(*Calculates the equilibrium constant K for a chemical equation typed in the form atpHl+de==hydroion+atpHO.*) energy=Solve [eq,del ; dG=energy[[l,l,2l]/.is->islist; Exp[-dG/(8.31451*.29815)11 atpkl=calckrx[at~Hl+de==hydro~on+atpHO,{0,.1,.25}1 1.81144 1 0

I2.51302

-7

, 3.4275 1 0

-7

}

TableForm[{at~kl,atpk2,adpkl,adpk2,~ikl,kref},TableHeadings> { {llatpkl", "atpk2". aadpklcl, "adpk2","piklt',"kref'I },iO, 1, .25 1 11

.

0 atpkl atpk2

-8

0.1

-7

2.51302 1 0 0.0000210082

1.81144 10 0.0000924186

-8

-7

adpkl

6.64366 1 0

adpk2

0.0000437761

pikl

6.05499 1 0

kref

0.291014

-8

2.92266 1 0

0.000117531 1.62565 10

0.25 3.4275 1 0

-7

0.000149099 -7 4.71512 10 0.000161669

-7

0.177606

2.23617 1 0

-7

0.151432

3.2 For the solution reaction A = B, assume that the standard Gibbs energy of formation of A is 20 kJ mol-' and of B is 18 kJ mol-' at 298.15 K. (a) For a reaction starting with a mole of A at a concentration of 1 M, plot the Gibbs energy of the mixture versus extent of reaction from zero to unity and identify the approximate extent of reaction at equilibrium. (b) Identify the equilibrium extent of reaction more precisely by plotting the derivative of the Gibbs energy of the mixture with respect to extent of reaction. (c) Calculate the equilibrium constant and verify the equilibrium extent of reaction. (a) The Gibbs energy of the reaction mixture is given by Clear [XI g = ( 1 - X ) * 2 0 + 1 8 * ~ (8.31451*10"-3) + *298.15* ((I-X) *LOg[l-X] +X*LOSf[XI) 2 0 (1 -

X)

+ 1 8 x + 2 . 4 7 8 9 7 ( ( 1-

X)

LOg[l - XI

+ x Lo~[xI)

Plot[g, {X, 0 , I}, Axesorigin-> { O , 15}, AxesLabel- {llg/molul, "G/kJ mol-l"}, PlotRange -f {15, 21}];

262

Mathernatica Solutions to Problems

0.2

0.4

0.6

0.8

'

1

S/mol

The approximate extent of reaction at equilibrium 298 K and 1 bar is 0.7. (b) The derivative of G with respect to x is given by dvt = D[g, -2

+

X]

2.47897

(-LOg[l

- XI

+ Log [ X I

Plot [dvt, {x, 0, l), PlotRange

-f

)

{ - l o , 101, AxesLabel+ { l l g / m o l r l , " d G / d C " } ]

i

10: 7.5:

5:

2.5: '

-2.5:

1

Elmo1

-5:

-7.5: -10-

(c) The equilibrium constant is given by k = d(1-x), and so the equilibrium extent of reaction is given k = Exp[ Exp[ (18 - 2 0 ) / ( ( 8 . 3 1 4 5 * 1 l o0 " "- 3 ) * 2 9 8 . 1 5 ) ] 0.44629

x=k/(l+k).

Chemical Equilibrium in One Phase Systems

263

0.308576

This agrees with the preceding plot. 3.3 Calculate the standard Gibbs energy changes and equilibrium constants in terms of species for the following reactions at 298.15 K and ionic strengths of 0, 0.10, and 0.25 M. Summarize the calculations in two tables. NAD- + H~(g) = N A D H ~ -+ H' (a) NADP3- + H2 (g) = NADPH4- + H+ (b) NAD- + NADPH4-= NADH2- + NADP3(c) CH3 CH2 OH + NAD- = CH3 C H O + NADH2- + H+ (d) CH3 C H O + NAD- + H 2 O = CH, C 0 2 + NADH2- + 2 H+ (e) C3 H7 NO2 + NAD- + H 2 0 = C3 H3 0-+ NADH2- + NH4 + H+ (f) The last reaction involves L-alanine and pyruvate. +

(BasicBiochemData2 has to be loaded) Since these reactants are all single species, calcdGis in the preceding problem can be used to calculate the function that gives the standard Gibbs energy of formation. The values at these three ionic strengths can be calculated using the assignment operation (/.). We can add the values for the products and subtract the values for the reactants to obtain the values of the standard Gibbs energy for the reaction. Finally, we can calculate the corresponding equilibrium constants and put them in a table. calcdGis [species-] := Module [ {dGzero, zi, isterm), (*This program calculates the function of ionic strength (is) that gives the standard Gibbs energy of formation of a species at298.15 K. The input is a list for the species that gives the standard Gibbs energy of formation, the standard enthalpy of formation,the electric charge, and the number of hydrogen atoms in the species. Energies are expressed in kJ mol*-l.*) dGzero = species[[l]]; zi = species [ [ 31 ] ; isterm=2.91482* (ziA2)*(isA.5)/ (1+1.6*isA.5); dGzero - isterm] hydroionis=calcdGis[hydro~onspl/.is->{O,.l,.25l (0, -0.612064,

-0.8096721

{0,

-0.809672)

-0.612064,

The Flatten is needed to remove the outer curly brackets in the BasicBiochemData2.

nadpredis=calcdGisCFlatten[nadpredspll/.is->{O,.l,.25};

264

Mathernatica Solutions to Problems -181.64 ethanolis={-181.64,-181.64,-181.641

{-181.64, -181.64, -181.64)

This had to be put in by hand because ethanol is not an ion. calcdGis[Flatten[acetaldehydesgll/.~s->{0,.1,.25~ -139. acetaldehydeis={-139.,-139.,-139.l;

calcdGis[Flatten[h2ospll/.is->~O,.1,.25l -237.19

h20is={-237.19,-237.19,-237.19};

calcdGis[Flatten[alaninesgll/.is->{o,.1,.25~ -371.

dGrxb=nadpredis+hydroionis-nadpoxis-h2gis; krxb=Exp[-dGrxb/(8.31451*.29815)];

dGrxc=nadredis+nadpoxis-nadoxis-nadpredis; krxc=Exp[-dGrxc/(8.31451*.29815)1;

dGrxd=acetaldehydeis+nadredis+hydroionis-ethanolis-nadoxis; krxd=Exp[-dGrxd/(8.31451*.29815)];

dGrxe=acetateis+nadredis+2*hydroionis-acetaldehyde~s-nadox~s-h20~~; krxe=Exp[-dGrxe/(8.31451*.29815)1; dGrxf=pyruvateis+nadredis+nh4is+hydroionis-alanineis-nadoxis-h2ois; krxf=Exp[-dGrxf/(8.31451*.29815)];

Table 1 Standard Reaction Gibbs Energies in kJ m o l - I at 298.15 K

Chemical Equilibrium in One Phase Systems

265

TableForml{dGrxa,dGrxb,dGrxc,dGrxd,dGrxe,dGrxf}rTableHeadings>C{"dGrxan,ildGrxblm, lldGrxcll, ndGrxd",i~dGrxei~,ildGrxfil}, {0,0.10,0.25}}]

dGrxa

0 22.65

0.1 20.2017

0.25 19.4113

dGrxb

25.99

21.0935

19.5126

dGrxc

-3.34

-0.891743

-0.101311

dGrxd

65.29

62.8417

62.0513

dGrxe

29.53

25.8576

24.672

dGrxf

79.26

75.5876

74.402

Table 2 Equilibrium constants at 298.15 K TableForml{krxa,krxb,krxc,krxd,krxe,krxf},TableHeadings> { { **krxa", lmkrxbllr ilkrxc", "krxdn,"krxe", "krxf " 1 ( 0 , O . 10,O. 25) > 1 krxa

0 0.000107625

0.1 0.000288953

0.25 0.00039747

krxb

0.0000279753

0.000201652

0.000381554

krxc

3.84715

1.43293

1.04171

krxd

-12 3.64546 10

-12 9.78736 10

-11 1.3463 10

krxe

-6 6.70807 10

0.0000295099

0.0000476083

krxf

-14 1.30115 10

-14 5.72398 10

-14 9.23451 10

These values agree with R. A. Alberty, Arch. Biochem. Biophys. 307, 8-14 (1993). 3.4 Plot the acid dissociation constant of acetic acid from 0 OC to 50 OC given that at 298.15 K, A f G o = 27.14 kJ mol-', Af H o = -0.39 kJ mol-', and Af Cp"= -155 J K-lmol-'. Assume zero ionic strength. A f F = (Af H" - A f G o )/T deltaS=(-390-27140)/298.15

-92.3361

-11.1059 +

46.906 298.15 + 18.6421 (1 - ___ - Log [ O .00335402 tl 1 t t ~

plot [ink,{ t, 273.15,323.15} .hesOrigin->{270, -11.02) ,hesLabel->{" T / K " , "AG"11 i

266

Mathematica Solutions t o Problems

AG

I " '

280

290

310

300

'

320

,"

T/K

Plot [Exp[lnk],{t, 273.15,323.15} ,AxesOrigin->{270,. 0000164) ,AxesLabel->{"T/K","K")I

;

0.00001760.0000174-

0.00001720.0000170.00001680.0000166.

I

' ' 2 8 0 ' 290 "

'

"

300 " .

"

"

'

310

320

T/K

\"

3.5 (a) Calculate the function of T that gives the values of the Debye-Huckel constant (Y at the temperatures in Table 3.1 in Section 3.7. Plot the data and the function. (b) Calculate the function of T for RTa. (c) Calculate the function of T for RT2 (&/dT), . (d) Use these functions to calculate these coefficients at 0, 10, 20, 25, 30, and 40 O C. (a) The Debye-Huckel constant (Y as a function of temperature: data=~~273.15,1.12938),C283.15,1.14717~,~293.15,1.16598},{298.15,1.17582~,{303.15,1.185 99},{313.15,1.20732})

CC273.15, 1.129381, I283.15, 1.147171, I293.15, 1.165981, C298.15, 1.17582), C303.15, 1 C313.15, 1.20732}} TableForm [data]

Chemical Equilibrium in One Phase Systems

273.15 283.15 293.15 298.15 303.15 313.15

1.12938 1.14717 1.16598 1.17582 1.18599 1.20732

alpha=Fit[data,Cl,t,tA2>,tl

-6 2 1.10708 - 0.00154508 t + 5.95584 10 t

a

280

290

300

T/K

310

(b) R T a as a function of temperature: rtalpha=Expand[8.31451*10A-3*t*alphal

0.00920485 t - 0.0'000128466t

2

-8

+ 4.95199 10

t

3

The factor 10"-3 converts the value of R from J to kJ. (c) R T ~( 8 a / 8 T ) as a function of temperature: rt2Dalpha=Expand[8.31451*10A-3*tA2*D[alpha,tlJ

2 -8 3 -0.0000128466 t + 9.90399 10 t

Take the derivative of RTalpha (d) Make a table col2=alpha/.t->{0,10,20,25,30,40~+273.15

{1.12942, 1.1471, 1.16597, 1.17585, 1.18603, 1.20729)

267

268

Mathematica Solutions to Problems

col3=rtalpha/.t->{0,10,20,25,30,40)+273.15

{2.56503, 2.70056, 2.84193, 2.91491, 2.98945, 3.14341) col4=rt2Dalpha/.t->{0,10,20,25,30,40~+273.15

I1.05994, 1.21837, 1.39106, 1.48294, 1.5786, 1.78158)

{{273.15, 283.15, 293.15, 298.15, 303.15, 313.15), {1.12942, 1.1471, 1.16597, 1.17585, 1.18603, 1.20729), {2.56503, 2.70056, 2.84193, 2.91491, 2.98945, 3.143411, {1.05994, 1.21837, 1.39106, 1.48294, 1.5786, 1.78158)) TableForm[Transpose[tab],TableHeadings->{None,{"T/K", l l a a ,"RTa", "RT"2 (da/dT)''I 11

T/K 273.15

a

1.12942

RTa 2.56503

RT"2 (aa/aT) 1.05994

283.15

1.1471

2.70056

1.21837

293.15

1.16597

2.84193

1.39106

298.15

1.17585

2.91491

1.48294

303.15

1.18603

2.98945

1.5786

313.15

1.20729

3.14341

1.78158

These values can be compared with the values in Table 3.1 in the text. 3.6 Calculate the standard Gibbs energies of formation of the three species of ATP at temperatures of 283.15 K, 298.15 K, 313.15 K and ionic strengths of 0, 0.10, and 0.25 M. (BasicBiochemData2 has to be loaded) ca1cdGTspCspeciesmat-,temp-,ionstr-l := Module[{dGzero, dGzeroT,dHzero,zi, nH, gibbscoeff, istermG,gfnsp},(*This program calculates the functions of T and ionic strength for the standard Gibbs energy of formation for all of the species in a reactant. The temperature, temp in K,can be specified in approximately the range 273.15 K to 313.15 K, and the ionic strength, ionstr in M, can be specified in the range 0 to 0.35 M. Lists of temperatures and ionic strengths can also be used. The standard Gibbs energies of formation in the output are in kJ molA-l. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 298.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the numbers of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gfnsp is alist of the functions for the species.*) {dGzero,dHzero,zi,nH} = Transpose[speciesmat]; gibbscoeff=9.20483*1OA-3*t-l.284668*lOA-5*tA2+4.95l99*lOA-8*tA3; dGzeroT=dGzero*t/298.15+dHzero*(l-t/298.15); istennG = gibbscoeff*(ziA2)*(isA.5)/(1 + 1.6*isA.5); istermG; gfnsp=dGzeroT gfnsp/.t->temp/.is->ionstr]

-

gat~=calcdGTsp[atpsp,298.15,0]

{-2768.1, -2811.48, -2838.18)

Chemical Equilibrium in One Phase Systems

269

{I-2768.1, -3619.21, -4, 12}, {-2811.48, -3612.91, -3, 13}, I-2838.18, -3627.91, -2, 141

This program is run three times at I = 0, 0.10, and 0.25 M. Tab1eFo~~ca1cdGTsptat~sp,~283.15,298.15,1eHeadings> { { "ATP-4'I, "HATP-3" I "H2ATP-2"1, { "283.15 K" ,"298.15 K" ,"3 13.15 K" 1 } ]

ATP-4

283.15 K -2810.92

298.15 K -2768.1

313.15 K -2725.28

HATP-3

-2851.8

-2811.48

-2771.16

H2ATP-2

-2877.91

-2838.18

-2798.45

Tab1eFormtca1cdGTs~tatpsp,(283.15,298.151eHead~ngs> { { "ATP-4" I "HATP-3", "H2ATP-2"1, E "283.15 K" ,"298.15 K" ,"313.15 K" 1 1I

ATP-4

283.15 K -2819.99

298.15 K -2777.89

313.15 K -2735.84

HATP-3

-2856.9

-2816.99

-2777.1

H2ATP-2

-2880.18

-2840.63

-2801.09

TableFormlcalcdGTsp[atps~,{283.15,298.15,313.15},.25],~TableHeadings> { { "ATP-4'I, "HATP-3 " ,"H2ATP-2" 1 ,{ "283 -15 K" ,"298.15 K" ,"313.15 K" 1 } I

ATP-4

283.15 K -2822.92

298.15 K -2781.06

313.15 K -2739.25

HATP-3

-2858.55

-2818.77

-2779.02

H2ATP-2

-2880.91

-2841.42

-2801.94

3.7 Calculate the adjustments to be subtracted from pH, obtained with a pH meter to obtain pH,= -log[H' and ionic strengths of 0,O. 10, and 0.25 M.

at 0 "C to 40 "C

The values of o in the Debye-Huckel equation are given by data={{273.15,1.12938),{283.15,1.14717},{293.15,1.16598},{298.15,1.17582~,~303.15,1.185

99),{313.15,1.20732)}

{{273.15, 1.12938}, {283.15, 1.14717}, (293.15, 1.16598}, {298.15, 1.175821, {303.15, 1.18599}, {313.15, 1.20732)) TableForm[datal

273.15 283.15 293.15 298.15 303.15 313.15

1.12938 1.14717 1.16598 1.17582 1.18599 1.20732

alpha=Fit [data,(1,t, t "2 } ,t]

-6 2 1.10708 - 0.00154508 t + 5.95584 10 t alpha

-6 2 t 1.10708 - 0.00154508 t + 5.95584 10

270

Mathematica Solutions to Problems

Equation 3.7-6 yields the following table: These are the adjustments to be subtracted from pH,to give pH,=

-

log H + ]

TableFonn[Trans~ose[alpha*isA.5/(Log[lO]*(l+l.6*isA.5))/.t-~{283.l5,298.l5,3l3.l5}/.~s>{O, .05, -1,.15, .2, .25)] ,TableHeadings->{{110",".05",".10t1,".15",'I .2O", ".25"}, {"lo C","25 C","40 C"))I

c

25 C 0

40 C 0

0.0820433

0.0841

0.0863484

.10

0.104609

0.107232

0.110098

.I5

0.119125

0.122111

0.125376

.20

0.129867

0.133122

0.136681

.25

0.138383

0.141852

0.145644

0

10 0

.05

3.8 Calculate the standard enthalpies of formation of the three species of ATP at 283.15 K, 298.15 K, and 313.15 K at ionic strengths of 0, 0.10, and 0.25 M.

(BasicBiochemData2 has to be loaded) Since we have a program to calculate standard Gibbs energies of formation, we can calculate the standard enthalpies of formation by use of the Gibbs Helmholtz equation. calcdHTsp [speciesmat,-,temp-, ionstr-1 := Module[{dGzero, dGzeroT,dHzero,zi, nH, gibbscoeff, istermG,gfnsp,hfnsp),(*This program first calculates the functions of T and ionic strength for the standard Gibbs energy of formation for all of the species in a reactant, and then uses the Gibbs Duhem equation to calculate the functions of T and ionic strength for the standard enthalpy of formation. The temperature, temp in &can be specified in approximately the range 273.15 K to 313.15 K, and the ionic strength, ionstr in M, can be specified in the range 0 to 0.35 M. Lists of temperatures and ionic strengths can also be used. The standard enthalpies of formation in the output are in kJ molA-l. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 298.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gfnsp is alist of the functions for the species. hfnsp is a list of the functions for the enthalpies of the species.*) {dGzero,dHzero,zi,nH) = Transpose[speciesmat]; gibbscoeff=9.20483*1OA-3*t-l.284668*lOA-5*tA2~4.95l99*lOA-8*t~3; dGzeroT=dGzero*t/298.15+dH~ero*(l-t/298.15); istermG = gibbscoeff*(ziA2)*(isA.5)/(1 + 1.6*isA.5); gfnsp=dGzeroT istennG; hfnsp=-tA2*D[gfnsp/t,t]; hfnsp/.t->temp/.is->ionstr]

-

calcdHTsplatpsp,298.15,01

{-3619.21, -3612.91, -3627.91)

These are the expected values for these three species at zero ionic strength.

{{-2768.1, -3619.21, -4, 12}, {-2811.48, -3612.91, -3, 13}, {-2838.18, -3627.91, -2, 14}}

Chemical Equilibrium in One Phase Systems

271

TableForm~calcdHTsp~atpsp,C283.15,298.15,313.15},01,T~1eHeadings> C C "ATP-4" ,"HATP-3 ' I , "H2ATP-2" 1,{ "283.15 K" ,"298.15 K" ,"3 13.15 K" 1 1 I

ATP-4

283.15 K -3619.21

298.15 K -3619.21

313.15 K -3619.21

HATP-3

-3612.91

-3612.91

-3612.91

H2ATP-2

-3627.91

-3627.91

-3627.91

This calculation is based on the assumption that the standard enthalpies of formation of the three species are independent of temperature, and so this is the expected result. TableForm[calcdHTsp[at~s~,{283.15,298.15,313.15},.l],TableHeadings> C C "ATP-4 ' I , "HATP-3" ,"H2ATP-2 " 1, { "283 -15 K" ,"298.15 K" ,"313.15 K" 1 1 I

ATP-4

283.15 K -3615.12

298.15 K -3614.23

313.15 K -3613.22

HATP-3

-3610.61

-3610.11

-3609.54

H2ATP-2

-3626.89

-3626.66

-3626.41

Even though the standard enthalpies of formation are independent of temperature at zero ionic strength, they are not independent of temperature at a finite ionic strength. The largest effect is for the -4 ion. TableForm[calcdHTsp[atpspr(283.15,298.15,313.15},.25l,TableHeadings> C I "ATP-4' I , " IiATP-3 'I, "H2ATP-2" 1, C "283 .15 K" ,"298.15 K" ,"313 .15 K" 1 1 1 ATP-4

283.15 K -3613.8

298.15 K -3612.62

313.15 K -3611.29

HATP-3

-3609.86

-3609.2

-3608.46

H2ATP-2

-3626.56

-3626.26

-3625.93

3.9 There are two ways to obtain values for the enthalpy coefficient in equation 3.6-5 as a function of temperature: (a) Calculate the derivative of the Gibbs energy coefficient divided by T. (b) Fit the enthalpy coefficients of Clarke and Glew to AT2 + BT3. Use both of these methods and make plots to compare these functions with the values in Table 3.1 (a) According to Problem 3.5, RTa is given by rtal~ha=9.20485*10A-3*t-l.28466*lOA-5*tA2+4.95l99*lOA-8*tA3

-8 3 0.00920485 t - 0.0000128466 t2 + 4.95199 10 t

Using the Gibbs-Helmholtz equation rt2Dalpha=Expand[tA2*D[rtalpha/t,tll

0. t

-

-8 3 0.0000128466 t2 + 9.90398 10 t

The following are the enthalpy coefficients given by Clarke and Glew.

272

Mathernatica Solutions to Problems {{273.15, 1.0751, {283.15, 1.2131, I293.15, 1.38451, (298.15, {303.15, 1.57751, {313.15, 1.811 TableForm Idatah]

273.15 283.15 293.15 298.15 303.15 313.15

1.075 1.213 1.3845 1.4775 1.5775 1.8

coefh

(b) Fit the Clarke and Glew enthalpy coefficients coefh=Fit Idatah, {tA2,tA3},tl

-0.0000132345 t

2

-7

+ 1.0045 10

3 t

Note -1.28466*1OA-5+9.9O398*10A-8tA3in (a), coefh/.t->{273.15,283.15,293.15,298.15,303.~5,313.15}

{1.05973, 1.21928, 1.39324, 1.48582, 1.58223, 1.78684)

These values can be compared with the table in (a).

Chemical Equilibrium in One Phase Systems

273

coefh

3.10 Plot the activity coefficients of ions with charges 1, 2 , 3, and 4 versus the ionic strength at 0 "C. Repeat these calculations at 25 "C and 40 "C. At 0 ° C gamma0[z~,is~l:=Module~O,(*Calculatesthe activity coefficient of an ion of charge z at 0 C as a function of ionic strength at 0 C . * ) Exp[-1.12942*(zA2)*(isA.5)/(l+l.6*isA.5)II

274

Mathematica Solutions to Problems

Y

l r

0.05

0.1

0.15

0.2

0.25

I/M

At 25 "C ganrma25[z-,is-]:=Module[{),(*Calculates the activity coefficient of an ion of charge z at 0 C as a function of ionic strength at 0 C.*) Exp[-1.17585*(zA2)*(isA.5)/(l+l.6*isA.5)II plot251=Plot [garmna25[ 1, is], {is,O, .25} ,PlotRange->{O, 1) ,AxesOrigin->{O,03 ,I+xesLab*l> { l l l / M 1 l , l1yt1} ,DisglayFunction->Identity]; plot 252=Plot [gamma25 [ 2, i s],{ is ,0 ,.25 1 ,PlotRange- > { 0,11, Axe sorigin-> { 0 1 0 3 ,Axes Labe1> ( l l I / M i l , 'iyii 1 ,DisglayFunction->Identity];

Chemical Equilibrium in One Phase Systems

275

Y 1 0.8

0.6 0.4

0.2

-

0.05

0.1

0.15

0.2

0.25

I /M

At 40 "C gamma40[z-,is-]:=Module[{},(*Calculates the activity coefficient of an ion of charge z at 0 C as a function of ionic strength at 0 C . * ) Exp[-1.20729*(zA2)*(isA.5)/(l+l.6*isA.5)II glot401=Plot[gamma40[1,is],{is,0,.25},PlotRange-~{O,1},AxesOrigin-~{O,O},AxesLabel> { "1/MI1,"y" 1, Di splayhnct ion->Identity]; glot402=Plot[gamma40[2,is],{is,0,.25},PlotRange-~{O,1~,AxesOrigin-~~O.O~.~e~Lab~~> { 1' I/MI',1s y" } ,Di splayFunction->Identity1; plot403=Plot[gamma40[3,~sl,{~s,0..25~,PlotRange->{O,l~,AxesOrigin->~O,O},AxesLabel> { I/MI1, y 1,Di SplayFunction->Identity1;

glot404=Plot[ganrma4O[4,is],{is,0,.25},PlotRange-~~O,l},AxesOrigin-~~OrO~,AxesLabel> { lmI/M1l, miyim} ,DisplayFunction->Identity1;

276

Mathernatica Solutions to Problems

Y l r

0.8 0.6

0.4 0.2

0.05

0.1

0.15

0.2

0.25

I/M

0.05

0.1

0.15

0.2

0.25

I/M

At 0 C and 40 C .

Y

Chapter 4 Thermodynamics of Biochemical Reactions at Specified pH 4.1 (a) Calculate Of G ofor the species of ATP at 298.15 K, pH 7, and I = 0.25. (b) Calculate a,G'" for ATP at 298.15 K, pH 7, and I = 0.25 M. (c) Plot & G o for ATP at 298.15 K, and I = 0.25 M versus pH. (d) Plot N,for ATP at I = 0.25 M versus pH. 4.2 (a) Calculate & H 0 for ATP at 298.15 K, pH 7, and I = 0.25 M. (b) Plot A f H o for ATP at 298.15 K, and I = 0.25 M versus pH. (c) Calculate the standard transformed enthalpy of formation at pH 7 and 0.25 M ionic strength at several temperatures in the range 273 K to 3 13 K. 4.3 (a) Calculate AI G'" in kJ mol-I at 298.15 K, pH 7, and I = 0.25 M for ATP + H 2 0 = ADP + Pi. (b) Calculate the corresponding Ar H'" . (c) Calculate the corresponding A , S " in J K-'mo1-l. (d) Calculate logK. (e) Plot the values of each of these properties versus pH at I = 0.25 M on the assumption that the standard enthalpies of formation of ions are independent of temperature. 4.4 (a) For ATP + H20 = ADP + Pi plot K' versus pH at ionic strengths of 0, 0.10, and 0.25 M. (b) Plot IogK' versus pH at ionic strengths of 0, 0.10, and 0.25 M. (c) Plot K versus ionic strength at pHs 5, 7, and 9. 4.5 For ATP + H20 = ADP + Pi plot A,N, versus pH at ionic strengths of 0, 0.10, and 0.25 M. 4.6 Calculate the standard transformed Gibbs energies of reaction for ATP + H20 = ADP + Pi at temperatures of 283.15 K, 298.15 K, and 313.15 K, at pHs 5 , 6,7, 8, 9, and ionic strengths of O,O.lO, and 0.25 M. 4.7 Calculate the standard transformed Gibbs energies of reaction at 298.15 K and the experimental pH and ionic strength for the reactions in the Goldberg and Tewari series of six critical reviews for which all the reactants are in BasicBiochemData2. Compare the calculated standard transformed Gibbs energies of reaction with the experimental values. At present there is not enough information to calculate the effects of temperature and metal ions, and so these effects are ignored. The three steps in this process are: (a) Make a table of the calculated standard transformed Gibbs energies of reaction. (b) Make a table of the relevant data in the Goldberg and Tewari Tables. (c) Make a table of the differences between the values of the standard transformed Gibbs energies of reaction calculated in part (a) and the experimental values in the Goldberg and Tewari tables. 4.8 Calculate the standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the binding of hydrogen ions for the ten reactions of glycolysis at 298.15 K, pHs 5, 6, 7, 8, and 9, and ionic strengths 0, 0.10, and 0.25 M. Also calculate these properties for the net reaction. 4.9 Calculate the standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the binding of hydrogen ions for the four reactions of gluconeogenesis that are different from those in glycolysis at 298.15 K, pHs 5 , 6, 7, 8, and 9 and ionic strengths 0, 0.10, and 0.25 M. Also calculate the properties of the net of pyruvate carboxylase and phosphoenolpyruvate carboxykinase reactions and the net reaction of gluconeogenesis. 4.10 Calculate the standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the binding of hydrogen ions for the pyruvate dehydrogenase reaction and the nine reactions of the citric acid cycle at 298.15 K, pHs 5, 6, 7, 8, and 9 and ionic strengths 0, 0.10, and 0.25 M. Also calculate these properties for the net reaction of the citric acid cycle, the net reaction for pyruvate dehydrogenase plus the citric acid cycle, and the net reaction for glycolysis, pyruvate dehydrogenase, and the citric acid cycle.

277

278

Mathematica Solutions to Problems

4.1 (a) Calculate afG'" for the species of ATP at 298.15 K, pH 7, and I = 0.25. (b) Calculate A,G'" for ATP at 298.15 K, pH 7, and I = 0.25 M. (c) Plot A f G o for ATP at 298.15 K, and I = 0.25 M versus pH. (d) Plot N,for ATP at I = 0.25 M versus pH. (BasicBiochemData2 has to be loaded)

(a) Use equation 4.4-10

dgsp -

0.5 2 2.91482 is (-nH + zi ) -PH - 2.47897 nH Log[lO 1 0.5 1 + 1.6 is

The data on the three species of ATP are in \the package. The basic data for species of ATP are given by atRsR {{-2768.1, -3619.21, -4, 12}, {-2811.48, -3612.91, -3, 13}, {-2838.18, -3627.91, -2, 14}} TableFOrm[atpSp] -2768.1 -2811.48 -2838.18

-3619.21 -3612.91 -3627.91

-4 -3 -2

12 13 14

The first row gives the standard Gibbs energy of formation, the standard enthalpy of formation, the charge number, and the number of hydrogen atoms of the species with the fewest hydrogen atoms. The standard transformed Gibbs energy of this species can be calculated by using the function in the first line of this problem. atpsgll2,lll

-2811.48 g1=atgsp~~~,~ll-~~*8.3l45l*.298l5*Log[lOA-7l-Z.9l482*((-4)A2-l2)*(.25A.5)/(l+l.6*.25A.5 1

-2291.86 ~~~~~pSg[[~,111-13*8.31451*.29815*L0g[10~-71-2.91482*((-3)~2-13)*(.25~.5)/(1+1.6*~.25~. 5))

-2288.81 g3=atgsg[[3,1]]-14*8.3l45l*.Z98l5*Log[lOA-7]-2.9l482*((-2)A2-l4)*(.25A.5)/(l+l.6*(.25A. 5))

-2270.I

(b) Use equation 4.5-1 to calculate A, G'" for the pseudoisomer group

Thermodynamics of Biochemical Reactions at Specified pH

279

-2292.5

calcdQRat[atpspl/.pH->7/.is->.25 -2292.5

This illustrates the convenience of the program calcdGmar.. (c) When the package BasicBiochemData2 is loaded, typing atp yields a function of pH and ionic strength as we have seen in (b).

.

Plot [ atp/ is- > .25, {pH, 5,9}, AxesLabel-> { " p H t l ,

I*\

!\

(TraditionalForm\.\ (A\-r\ ) G ' \ "o\ ) I' 1 1 ;

A, G"

(d) Equation 4.7-3 shows that the average number of hydrogen atoms in a reactant is given by (lRTln(l0)) times the derivative of the standard transformed Gibbs energy of the reactant. First we calculate the function of pH at ionic strength 0.25 M

-0.403393 - 2 . 4 7 8 9 7 Log [E

(-2830.08

- 34.7056 Log[lO

E

-0.403393

(-2808.24

-

3 2 . 2 2 6 6 LOg[lO

E

-0.403393

(-2771.34

- 2 9 . 7 4 7 7 LOg[lO

-PH

I) + -PH

]'I

-PH

I)

+

280

Mathematica Solutions t o Problems

(-2.47897

-32.2362

(

E

0.403393 (-2830.08 - 34.7056 LOg[lO

-PH I)

29.9336

E

E (E

0.403393 (-2808.24 - 32.2266 L ~ g [ l O - ~ ~ l ) 27.631

-0.403393 (-2830.08

E

) )

/

0.403393 (-2771.34 - 29.7477 Log[lO-PHl) -

34.7056 LOg[lO

-PH

I) +

-0.403393 (-2808.24 - 32.2266 L ~ g [ l O - ~ ~ l )

E

-0.403393 (-2771.34 - 29.7477 L ~ g [ l O - ~ ~ l ) )

Plot[Evaluate[(l/(8.3l45l*.298l5*Log[lO]))*D[fpH,pH]l,{pH,5,9},~esLabel> {lmpH1l, 'I\ !\ (N\-H\)''1 I ; NH

4.2 (a) Calculate A f H o for ATP at 298.15 K, pH 7, and I = 0.25 M. (b) Plot & H a for ATP at 298.15 K, and I = 0.25 M versus pH. (c) Calculate the standard transformed enthalpy of formation at pH 7 and 0.25 M ionic strength at several temperatures in the range 273 K to 313 K on the assumption that the standard enthalpies of formation of ions are independent of pH.. (BasicBiochemData2 has to be loaded) (a) There are two different kinds of programs to make this calculation. The program calcdHmat calculates the equilibrium mole fractions of the species and the standard transformed enthalpies of formation of the species and calculates the mole fraction weighted average. The program calcdHTgp calculates the standard transformed Gibbs energy of formation of the reactant as a function of pH, ionic strength, and temperature and uses the Gibbs-Helmholtz equation to calculate the standard transfromed enthalpy of formation of the reactant.

Thennodynamics of Biochemical Reactions at Specified pH

281

calcdI-hnat [ speciesmat-] := Module[{dHzero, zi, nH, dhfnsp, dGzero, pHterm, isenth, dgfnsp, dGreactant, ri}, (*This program produces the function of ionic strength (is) that gives the standard transformed enthalpies of fonnation of the specie at 298.15 K. It then calculates the standard transformed Gibbs energy for the reactant and the equilibrium mole fractions of the species. The function of pH and ionic strength for the standard transformed enthalpy of formation of the reactant is calculated by a dot product. The input is a matrix that gives the standard Gibbs energy of formation, the standard enthalpy of formation, the electric charge'and the number of hydrogen atoms in the species in the reactant. There is a row in the matrix for each species of the reactant. Energies are expressed in kJ molA-l.*) {dGzero, dHzero, zi, n H ) = Transpose[speciesmat] ; isenth=1.4775* ((zi"2) -nH)*(isA.5) / (1+1.6*isA.5); dhfnsp dHzero+isenth; (*Now calculate the functions for the standard Gibbs energies of formation of the species.*) pHterm = nH* 8.31451 * .29815 *Log [loA -pH] ; gpfnsp = dGzero-pHterm-isenthe (2.91482/1.4775); (*Now calculate the standard transformed Gibbs energy of formation for the reactant.*) dGreactant = -8.31451* .29815*Log[Apply[Plus, Exp[-l*gpfnsp/ (8.31451* .29815)]]]; (*Now calculate the equilibrium mole fractions of the species in the reactant and the mole fraction-weighted average of the functions for the standard transformed enthalpies of the species.*) ri = Exp [ (dGreactant - gpfnsp) / (8.31451 * -29815)] ; ri.dhfnsp] fnh=calcdHmat[atpspl/.is->.25/.pH->7 -3616.89

calcdHTgp [speciesmat-I := Module[{dGzero, dGzeroT,dHzero,zi, nH, gibbscoeff,pHterm, isterm,gpfnsp,dGfnl,(*This program first produces the function of T (in Kelvin), pH and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species). It then uses the Gibbs-Helmholtz equation to calculate the function for the standard transformed enthalpy of formation of the pseudoisomer group. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 298.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the transformed Gibbs energies of the species. Energies are expressed in kJ molA-l. The value of the standard transformed enthalpy of formation can be calculated at any temperature in the approximate range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic strength in the range 0 to 0.35 m by use of the assignment operator(/.).*) {dGzero,dHzero,zi,nH}=Transpose[speciesmatl; gibbscoeff=9.20483*1OA-3*t-l.284668*lOA-5*tA2+4.95l99*lOA-8*tA3; dGzeroT=dGzero*t/298.15+dXizero*(l-t/298.15); pHterm = nH*8.31451*(t/1000)*Log[1OA-pHI; istermG = gibbscoeff*((ziA2) - nH)*(isA.5)/(1 + 1.6*isA.5); gpfnsp=dGzeroT - pHterm - istermG; dGfn=-8.31451*(t/100O)*Log[App~y[Plus,Exp[-l*gpfnsp/(8.3l45l*(t/lOOO~~lll; -tA2*DtdGfn/t,tll -3616.89

282

Mathematica Solutions to Problcms

This second program has the advantage that the standard transformed enthalpy of formation can be calculated at other temperatures. (b) This second program can be used to construct a plot of the standard transformed enthalpy of formation as a function of

PH.

(c) This second program can be used to calculate the standard transformed enthalpy of formation at several temperature

{-3617.28, -3616.89, -3616.681

This calculation is based on the assumption that the standard enthalpies of formation of the ions at zero ionic strength are independent of temperature. However, at finite ionic strength there is a small electrostatic effect on the enthalpy. 4.3 (a) Calculate A, G'" in kJ m o l - 1 at 298.15 K, pH 7, and I = 0.25 M for ATP + H20 = ADP + P,. (b) Calculate the corresponding A,H'" . (c) Calculate the corresponding A,S'" in J K - l m o l - l . (d) Calculate IogK'. (e) Plot the values of each of these properties versus pH at I = 0.25 M.

(BasicBiochemData2 must be loaded) calctrGerx[e~,pHlist_,islislist~]:=Module[{energy},(*Calculates the standard transformed Gibbs energy of reaction in kJ molA-l at specified p H s and ionic strengths for a biochemical equation typed in the form atp+hao+de==adp+pi. The names of the reactants call the appropriate functions of pH and ionic strength. pHlist and islist can be lists. This program can be used to calculate the standard transformed enthalpy of reaction by appending an h to the name of each reactant.*) energy=Solve[eq,del; energy[[1,1,2ll/.pH->pHlist/.is-~~sl~st]

(a) Calculate the standard transformed reaction Gibbs energy

-36.0353

(b) Append h to the name of each reactaant to obtain its standard transformed reaction enthalpy

Thermodynamics of Biocheniical Reactions at Specified pH

-23.0327

(c) The standard transformed entropy of reaction at pH 7 and I = 0.25 M is given by (-23.03+36.07)*1000/298.15 43.7364

(d) The base 10 logarithm of the apparent equilibrium constant is given by Log[~0.Exp~-dg298pH7is25/(8.31451*.29815)11 6.31308

(e) Plots Plot[calctrGerx[atp+h2o+de==adp+pi,~H,.25],{pH,5,9~,AxesLabel> { tlpH1l, I 1 \ !\ (TraditionalForm\ \ (A\-r\1 G' \ ^o\) 'I 1 1 ;

.

A, G

l o

Plot[calctrGerx[atph+h2oh+de==ad~h+p~h,pH,.25l,{pH,5,91,~esLabel,Axesorigin->{5, -27 1 I ; > { llpHtl, a * \ !\ (TraditionalForm\'\ (A\-r\) HI \^o\)

283

284

Mathernatica Solutions to Problems A, H

l o

6

7

8

9 '

PH

~lot[(calctrGerx[atph+h20h+de==adph+pih,pH,.251calctrGerx[atp+h2o+de==ad~+p~,pH,.251~~.29815,~pH,5,9~,~~sLab~l> { i t p H m i I,* \ !\ (TraditionalForm\'\ (A\-r\) S ' \ " O \ ) "1 1 ;

a,

s

l o

As the pH increases, the change in the transformed enthalpy becomes less favorable for hydrolysis, but the effect is small. On the other hand the transformed entropy increases rapidly with pH and causes the equilibrium to move further to the right. calck~rime[eg_,~Hlist~,~slist~l:=Module[{energy,dG},(*Calculates the apparent equilibrium constant K' at specified p H s and ionic strengths for a biochemical equation typed in the form atp+hao+de==adp+pi. The names of the reactants call the appropriate functions of p H and ionic strength. pHlist and islist can be entered as lists.*) energy=Solve[eq,del; dG=energy[[l,l,211/.pH->pHlist/.is->islist; E~p[-dG/(8.31451*.29815)]1 Plot[Log[lO,calckprime[atp+h2o+de==adp+p~,pH,.25ll,(~H,5,9~,~esOrigin> (5,5.5 1, AxesLabel-> ( l m p H 1 s"LogK' , "1 I ;

Thermodynamics of Biochemical Reactions at Specified pH

285

LogK'

6

7

8

'

9

PH

4.4 (a) For ATP + HzO = ADP + Pi plot K versus pH at ionic strengths of 0, 0.10, and 0.25 M. (b) Plot IogK' versus pH at ionic strengths of 0, 0.10, and 0.25 M. (c) Plot K versus ionic strength at pHs 5 , 7, and 9. (BasicBiochemData2 has to be loaded) ca~ckprime[e~,pH~ist_,islislist~]:=Module[{energy,dG},(*Calculates the apparent equilibrium constant K' at specified p H s and ionic strengths for a biochemical equation typed in the form atp+hao+de-=adp+pi. The names of the reactants call the appropriate functions of pH and ionic strength. pHlist and islist can be entered as lists.*) energyesolve [eq,de] ; dG=energy~[l,l,211/.pH->pHlist/.is->islist; E~p[-dG/(8.31451*.29815)11

286

Mathematica Solutions t o Problems

K' 1x10~

8x106

6x106

4x106

2X1O6

I

.

,

,

,

,

6

'

a

7

9

PH

The upper curve is for zero ionic strength.

Show[plotlogKp00,plotlogKgl0,glotlotlogK~25,PiotRange-~{5,8.5},~esOrigin> { 5 , 5 1, AxesLabel > { llpH", "1ogK I Is}, Di splayFunct ion- > $DiSplayFunction] ;

-

logK'

7.5-

7-

5-51 I

.

,

/

,

I

6

,

,

,

,

,

7

,

.

,

8

'

9

PH

The upper curve is for zero ionic strength. (c) In order to compare the ionic strength effects, the calculated apparent equilibrium constants are divided by the value at zero ionic strength at that pH.

Thermodynamics of Biochemical Reactions at Specified pH

K' (I)/ K ' (I=O)

l r

t . , , . , . . . . , . . , . , , , , 0.05

0.1

0.15

I

,

.

.

0.2

.

,

.

0.25

,

.

1

0.3

I/M

The lowest curve is for pH 5.

4.5 For ATP + H 2 0 = ADP + Pi plot ArNH versus pH at ionic strengths of 0, 0.10, and 0.25 M. (BasicBiochemData has to be loaded) calckprimele~,pHlist_,islist_l:=Module[{energy,dG),(*Calculates the apparent equilibrium constant K' at specified p H s and ionic strengths for a biochemical equation typed in the form atp+h2o+de==adg+pi. The names of the reactants call the appropriate functions of pH and ionic strength. pHlist and islist can be entered as lists. * ) energy=Solve[eq,de]; dG=energy[[l,l,2]]/.pH->pHlist/.is->islist; E~p[-dG/(8.31451*.29815)]1 kprime00=calckprime[atp+h2o+de==adp+pi,p€I,O];

287

288

Mathematica Solutions to Problems nH10= (-1/Log1101 ) *D [LogIkprimelOI ,pH]; plotnH10=Plot[nH10,{~H,5,9},Disp~ayFunction-~Identityl;

kprime25=calckprime[atp+h20+de==adp+pi,pH,.251; nH25=(-1/Log[101 )*D[Loglkprime251,PHI;

plotnH25=Plot[nH25,{~H,5,9},D~splayFunct~on->Ident~tyl; Show [plotnHOO,plotnH1O,plotnH25 ,AxesLabel->Cm'pKtl, >(5,-1},DisplayFunction->$Disp~ayFunction];

ArNH

I'

1, AxesOrigin-

a, NH

ot

4.6 Calculate the standard transformed Gibbs energies of reaction for ATP + H z O = ADP + P, at temperatures of (a) 298.15 K, (b) 283.15 K, and (c) 313.15 K, at pHs 5 , 6, 7, 8, 9, and ionic strengths of 0, 0.10, and 0.25 M.

(BasicBiochemData2 has to be loaded) (a) Calculations at 298.15 K calctrGerx[e~,pHlist_ri8lislist~]:=Module[{energy},(*Calculates the standard transformed Gibbs energy of reaction in kJ molA-l at specified ~ H Sand ionic strengths for a biochemical equation typed in the form atp+hao+de==adp+pi. The names of the reactants call the appropriate functions of pH and ionic strength. pHlist and islist can be lists. This program can be used to calculate the standard transformed enthalgy of reaction by appending an h to the name of each reactant.*) energy=Solve[eq,del; energy[[1,1,2]l/.pH->~H1ist/.is-~islist] dGerx298=calctrGerx[atp+h2o+de==adp+pi,{5,6,7,8,9},~0,.1,.25}1;

TableForm[Transpose[dGerx298],TableHeadings-> {"I =. 0 M " , " I

M"}, ( " p H 5","pH 6","pH 7","pH 8","pH 9 " } } 1

= 0.10 M " , " I

I = O M

PH 5 -35.299

PH 6 -35.9137

PH 7 -37.6048

PH 8 -42.5001

PH 9 -48.2933

I = 0.10 M

-33.2951

-33.8717

-36.5

-41.4784

-47.0983

0.25 M

-32.5633

-33.2166

-36.0353

-41.0742

-46.7021

I

z

= 0.25

Thermodynamics of Biochemical Reactions at Specified pH

289

To make the calculation at the other temperatures, we can use calcdGHT to produce the function of T, pH and ionic strength that will give A G O and A H o at other temperatures. calcdGHT [speciesmat-1 := ModuleIEdGzero, dGzeroT,dHzero,zi, nH, gibbscoeff,pHterm, isterm,gpfnsp,dGfn,dHfn),(*This program produces the function of T (in Kelvin), pH and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species) and the standard transformed enthalpy. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 298.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the transformed Gibbs energies of the species. The output is in the form {dGfn,dHfn), and energies are expressed in kJ molA-l. The values of the standard transformed Gibbs energy of formation and the standard transformed enthalpy of formation can be calculated at any temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic strength in the range 0 to 0.35 m by use of the assignment operator(/.).*) {dGzero,dHzero,zi,nH}=Transpose[speciesmat]; gibbscoeff=9.20483*1OA-3*t-l.284668*lOA-5*tA2+4.95l99*lOA-8*tA3; dGzeroT=dGzero*t/298.15+dHzero*(l-t/298.15); pHterm nH*8.31451*(t/1000)*LOg[10A-pH]; istennG = gibbscoeff*((ziA2) nH)*(isA.5)/(1 + 1.6*isA.5); gpfnsp=dGzeroT pHterm istennG; dGfn=-8.31451*(t/100O)*Log[A~ply[Plus,Exp[-l*gpfnsp/(8.3l45l*(t/lOOO)~lll; dIifn=-tA2*D[dGfn/t,t]; {dGfn,dHfn)l

-

-

-

(b) Calculate the standard transformed Gibbs energies of of the reactants and the reaction at 283.15 K. atp283=calcdGHT[atpspl [[111/.t->283.15;

adp283=calcdGHT[adpspl ttlIl/.t->283.15;

dGerx283=calctrGerx[at~283+h20283+de==adp283+pi283,~5,6,7,8,9~,~0,.1,.25~1 {{-34.6913, -32.9147, -32.2468}, {-35.3381, -33.4522, -32.8351}, {-36.9415, (-41.4708, -40.4698, -40.0894}, I-46.9055, -45.7905, -45.4228}}

TableForm[Transpose[dGerx283] ,TableHeadings->{{'I M"),{"pH 5","pH 6","pH 7","pH 8","gH 9")>1

= 0 M1a,"I = 0.10 M " , " I

I = O M

PH 5 -34.6913

PH 6

-35.3381

PH 7 -36.9415

PH 8 -41.4708

PH 9 -46.9055

I = 0.10 M

-32.9147

-33.4522

-35.8386

-40.4698

-45.7905

I = 0.25 M

-32.2468

-32.8351

-35.3814

-40.0894

-45.4228

(c) Calculate the standard transformed Gibbs energies of the reactants and the reaction at 313.15 K. atp313=calcdGHT[atpspl ~[111/.t->313.15;

adp313=calcdGHT[adpspl [[lIl/.t->313.15;

-35.8386,

= 0.25

-:

290

Mathematica Solutions to Problems

dGerx313=ca1ctrGerx[atg313+h20313+h2o313+de==adp313+p~313,~5,6,7,8,9~,~0,.1,.25~1

{{-35.9046, -33.6656, -32.8677}, {-36.4876, -34.2845, -33.58951, 1-38.272, -37.1598, -3f {-43.5265,-42.482, -42.0518}, {-49.6803, -48.4002, -47.973611 TableFonn[Transpose[dGerx313],TableHeadings->{{~'I = 0 M " , " I M"),{"pH 5","pH 6","pH 7","pH 8","pH 9 " ) ) l

= 0.10 M " , " I

PH 5

PH 6

-36.4876

PH 7 -38.272

PH 8 -43.5265

PH 9 -49.6803

I = 0.10 M

-33.6656

-34.2845

-37.1598

-42.482

-48.4002

I = 0.25 M

-32.8677

-33.5895

-36.6852

-42.0518

-47.9736

I = O M

-35.9046

= 0.25

Since the hydrolysis of ATP evolves heat, Le Chatelier's principle says raising the temperature will cause the reaction to go less far to the right. But at 3 13 K the transformed Gibbs energy of reaction is more negative. To apply Le Chatelier we have to look at the apparent equilibrium constants. At pH 7 and ionic strength 0, we obtain

6 6.63414 10

6 3.9283 10 k313=Exg[38.31/(8.31451*.31315)1

6 2.45525 10

These apparent equilibrium constants are in accord with what we expect.

4.7 Calculate the standard transformed Gibbs energies of reaction at 298.15 K and the experimental pH and ionic strength for the reactions in the Goldberg and Tewari series of six critical reviews for which all the reactants are in BasicBiochemData2. Compare the calculated standard transformed Gibbs energies of reaction with the experimental values. At present there is not enough information to calculate the effects of temperature and metal ions, and so these effects are ignored. The three steps in this process are: (a) Make a table of the calculated standard transformed Gibbs energies of reaction. (b) Make a table of the relevant data in the Goldberg and Tewari Tables. (c) Make a table of the differences between the values of the standard transformed Gibbs energies of reaction calculated in part (a) and the experimental values inthe Goldberg and Tewari Tables. (BasicBiochemData has to be loaded)

(a) Make a table of the calculated standard transformed Gibbs energies of reaction. calcrow[eg, pHlist-, islist-, rx-] := Module[{energy, do, gvector}, (*Calculates the standard transformed Gibbs energy of reaction for a specified reaction at specified p H s and a single ionic strength. It then prepends the reaction without the +de=. This second form of the reaction must be in quotation marks.*) energy = Solve [eq, de] ; dG=energy[[l, 1, 211 /. pH-tpHliSt /. is+islist; gvector = Flatten[Map[NumberForm[#, {a, 2}] &, {dG}, {2}]]; Prepend [gvector, 1x1 3

Thermodynamics of Biochemical Reactions at Specified pH

glxlxlxl= calcrow[ethanol+nadox+de::acetaldehyde+nadred, ; 7, .25, l~ethanol+nadox:-acetaldehyde+nadredl'] glxlxlx26 = calcrav[glycolate + nadox + de == glyoxylate + nadred. 7.8, -03, llglycolate+nadox=gloxylate+nadred"]; glxlxlx27b = calcrow [lactate+ nadox + de == pyruvate + nadred, 6.8, -05, **lactate+nadox=pyruvate+nadred"];

glxlxlx40calcrow[malate+nadgox+h2o+de==pyruvate+nadgred+co2tot,7,.25, *1malate+nadpox+h20=pyruvate+nadgred+co2tot1ml;

glxlxlx67= calcrow[mannitolD+nadox+de:=fructose+nadred,8.O5,.O5,

"mannitolD+nadox=fructose+nadred"l;

glxlxlx79= calcrow[glycolate+nadpox+de=:glyo~late+nadpred,7.92,.1, **glycolate+nadpox=glyoxylate+nadpred"l; glxlx99x7= calcrow~lactate+oxaloacetate+de..malate+py~vate,7~8,.1, ~llactate+oxaloacetate=malate+~yruvatell I;

glx4xlxl = calcrow[alanine+nadox+h2o+de=:pyruvate+nadred+ammonia, 7.97, -1, "alanine+nadox+h2o=pyruvate+nadred+ammonia"]; glx4xlx2 = calcrow[glutamate+nadox+h2o+de == ketoglutarate+nadred+ammonia, 6.9, .24, "glutamate+nadox+h2o=ketoglutarate+nadred+ammonia"]; glx4xlx3 = calcrow [glutamate+ nadpox + h20 + de == ketoglutarate + nadgred + ammonia, 7, -47. ~1glutamate+nadpox+h2o=ketoglutarate+nadgred+anrmonia"]; glx4xlxlO = calcrow[glycine+nadox+h2o+de=:glyoxylate+nadred+ammonia, 6.4, .08, *~glycine+nadox+h20=glyoxylate+nadred+ammonia~~];

291

292

Mathematica Solutions to Problems glx6xlxl= calcrow[nadox+nadpred+de=:nadred+nadpox,7.5,.1, mlnadox+nadpred=nadred+nadpoxll 1; glx6x4x2= calcrow[nadpox+2*glutathionered+de=:nad~red+glutathioneox,6.9,.25, "nadpox+2*glutathionered=nadpred+glutathioneo~~~]; glx6x4x5= calcrow[nadpox+thioredoxinred+de==nadpred+thioredoxinox,7,.1, 11nadpox+2*thioredoxinred=nad~red+thioredoxinox~~l; g2x3xlx54= ca~crow[acetylcoA+formate+de==coA+pyruvate,7.2,.O5, "acetylcoA+formate=c~A+pyruvate~~ 1;

g2x6xlx35= calcrow[glycine+oxaloacetate+de==glyoxylate+aspartate,7.1,.1, llglycine+oxaloacetate=glyoxylate+asgartatemtl;

g2x7xlx23= calcrow[atp+nadox+de==adp+nadpox,6.1,.1, llatp+nadox=adp+nadpox" I; g2x7x4x3= ca1crow[2*adp+de==amp+atp,7.41..04, "2*adp=amp+atpm11 ; g3xlx3xl= calcrow[amp+h2o+de~:adenosine+pi,8.86,.3, "amp+h2o=adenosine+pi"1 ; g3xlx3xlb= calcrow[fructose6phos+h2o+de:=fructose+pi,8.4,.29, ~~fructose6phos+h2o=f ructose+piall ; g3xlx3xlc= calcrow[glucose6phos+h2o+de=:glucose+p~,6.99,.25, 11glucose6phos+h20=glucose+pi"l ;

Thermodynamics of Biochemical Reactions at Specified pH

293

g3x2xlx3= calcrow[maltose+h20+de=:2*glucoser5,.01, 1*maltose+h20=2 *glucose" ] ; g3x2xlx23= calcrow[lactose+h2o+de:~glucose+galactoser5.65,.1, 111actose+h20=glucose+galactose1~l; g3x2x2x4= calcrow[amp+h2o+de==adenine+ribose5phos,8,.1, 1*amp+h20=adenine+ribose5phos 1; g3x2x2x7 = calcrow[adenosine+h20+de==adenine+ribose,7,.1, nadenosine+h20=adenine+ribosenl; g3x5xlx2= calcrow[glutamine+h2o+de==glutamate+ammoniar5.5,.1, 11glutamine+h20=glutamate+ammonia" I; g4xlx3xl= calcrow[citrateiso+de == succinate+glyoxylate, 7.7, .l, llcitrateiso=succinate+glyoxylatelm]; g4xlx3x6 = calcrow [citrate + de =: acetate

+ oxaloacetate, 7,

.2, ~mcitrate=acetate+oxaloacetate"] ;

g4xlx3x7 = calcrow[oxaloacetate+acetylcoA+h2o+de == citrate+coA, 7.05, .25, l~oxaloacetate+acetylcoA=citrate+coA"]; g4Xlx99x1 = calcrow [tryptophaneL + h20 + de == indole + pyruvate + ammonia, 7.97, .l, "tryptophaneL+h20=indole+pyruvate+ammonia~~]; g4x2xlx2

calcrow [ fumarate + h20 + de =: malate, 7.3, .l, "fumarate+h20=malate"] ;

g4x2xlx3 calcrow[citrate

+ de =: aconitatecis + h20, 7.4, .l,

1gcitrate=aconitatecis+h20"] ;

g4x3xlxl= calcrow[aspartate + d e =: fumarate + ammonia, 7.37, .l, llaspartate=fumarate+ammonia"] ; g5x3xlx5

calcrow [glucose + de

fructose, 7.5, -1, ~ l g l ~ ~ o s e = f r u ~ t;~ s e " ]

: :

g5x3xlx5b = calcrow [xylose + de == xylulose, 8.7, .l, ~lxylose=xylulose~l] ; g5x3xlx7 = calcrow[mannose

+ de == fructose, 7, .05, lmmannose=fructose''] ;

g5x3xlx9 = calcrow[glucose6phos + d e =: fructose6phos, 8.7, .3, mmglucose6phos=fructose6ghos"]; ~~5~3x1 = calcrow[lyxose ~15 + de == xylulose, 7, .06, ~*lyxose=xylulose~t] ; g5x3xlx20 = calcrow[ribose

+ de == ribulose, 7.4,

.04, llribose=ribulose"] ;

294

Matliematica Solutions to Problems

g5x3xlxa = calcrow[mannose + d e E: fructose, 7.6, -02, ~~mannose=fructose~'] ; gsx4x2x2 = calcrow[glucoselphos + d e == glucose6phos, 8.48, .l, ~1glucoselphos=glucose6phos~~]; g5x4x2x7 =calcrow[riboselphos+de =:ribose5phos, 7, .25, ~~riboselphos=ribose5ghos"l; g6x2xlxl= calcrow[atp+acetate+coA+de== amp+ppi+acetylcoA, ; 7, .25, "atp+acetate+coA=amg+ppicacetylcoA~l] g6x3xlx2 = calcrow[atp + glutamate + ammonia + de =: adp + p i + glutmine, 7, -3, llatp+glutamate+ammonia=adp+pi+glutaminel'] ; g6x4xlx1 = calcrow [atp + pyruvate + co2tot + de EE adp + p i + oxaloacetate, 7.4, .02, ~~atp+pyruvate+co2tot=adp+pi+oxaloacetate~']; TableFonn [ {glxlxlxl, glxlxlx26, glxlxlx27b, glxlxlx37, glxlxlx39, glxlxlx40, glxlxlx42, glxlxlx67, glxlxlx79, glxlX99x7, glx2xlx2, glx2xlx101 glx2xlx43, glx4Xlx1, g 1 ~ 6 ~ 4 ~g 21 ,~ 6 ~ 4 ~g2~3X1X54, 5, g2~4~1~7, g 1 ~ 4 ~ 1 ~g 21 ,~ 4 ~ 1 ~g 3l ,~ 4 ~ l ~ glx6xlxlr lO g2x4xlx8, g2x4x2x1, g2x6xlx1, g2x6xlx2, g2x6x1x35, g2x7xlx1, g2x7xlx23, g2x7x4x3, g3xlx3x1, g3xlx3xlb, g3xlx3xlc, g3x1x3x1df g3xlx3xle, g3x2xlx3, g3x2xlx23, g 3 ~ 2 ~ 2 ~g 43 ,~ 2 ~ 2 ~g 73 ,~ 5 ~ 1 ~ g2 4, ~ 1 ~ 3 ~g 1 4 ~, 1 X 3 ~ 6g4X1X3X7, , g4XlX99X1, gdX2XlX2, g4x2xlx3, g4x3xlx1, g5x3xlx5, g5x3x1x5bl g5x3xlx7, g5x3xlx9, g5x3xlx15, g5x3xlx20, g5x3xlxa, g5x4x2x2, g5x4x2x7, g6x2xlx1, g6x3xlx2, g6x4xlxl}, m11.1.1.26m1,111.1.1.27b", "1.1.1.37", "1.1.1.39", TableHeadings + {{mll.l.l.lll, "1.1.1.40", "1.1.1.42", "1.1.1.67", "1.1.1.79", "1.1.99.7", "1.2.1.2", 1.2.1. loi*, 1.2.1.43", 1.4.1. lit, 1.4.1.2 n, n 1.4.1.3", 1.4.1. l o r i , "1.6.1. l", I* 1.6.4 .2 ' I , 1 .6.4.5 1 1 , 2 .3 .1.54", 1- 2 . 4 1 .7 'I, 18 2 .4.1.8 2 -4.2-1 2 .6.1. l", "2.6.1.2", 1i2.6.1.35in,112.7.1.111,"2.7.1.23". ii2.7.4.3ii,"3.1.3 .l", "3 .l. 3 .lb", "3.1.3.1~" , "3.1.3. ld", "3.1.3. le", "3.2.1.3", "3 .2.1.23", "3.2.2.4", n 3.2.2.7 'I, 1~3.5.1.2*', 1'4.1.3. l", 4.1.3.61'~ 4.1.3.7 It4.1.99. l", I* 4.2.1.2", 11 4.2.1.3 11, 1~4.3.1.1" , 5.3 1 - 5'I, "5 .3.1.5bi*, 5 .3 -1.7 I@,In 5.3 1 - 9 "5 .3 1 .15", 6.2.1.1 " , "6.3 1 .2", 'I 6.4.1.1" } , "5.3.1.2 0 , l1 5.3.1. aim, 5.4.2.2 'I, In 5.4.2.7". {llReactionpl, "Calc G 1 l l } } , Tablespacing - > {I, l}]

.

.

11,

11

. .

1.1.1.1

Reaction ethanol+nadox==acetaldehyde+nadred

Calc G ' 22.095

1.1.1.26

glycolate+nadox=gloxylate+nadred

38.896

1.1.1.27b

lactate+nadox=pyruvate+nadred

26.3652

1.1.1.37

malate+nadox=oxaloacetate+nadred

28 -2639

1.1.1.39

malate+nadox+h2o=pyruvate+nadred+co2tot

4.45812

1.1.1.40

malate+nadpox+h2o=pyruvate+nadpred+co2tot

1.71088

1.1.1.42

citrateiso+nadpox+h2o=ketoglutarate+nadpred+co2tot-3.83041

1.1.1.67

mannitolD+nadox=fructose+nadred

1.88013

1.1.1.73

glycolate+nadpox=glyoxylate+nadpred

38.2358

1.1.99.7

lactate+oxaloacetate=malate+pyruvate

-4.92266

1.2.1.2

formate+nadox+h2o=co2tot+nadred

-15.1398

1.2.1.10

acetaldehyde+coA+nadox=acetylcoA+nadred

-13.861

1.2.1.43

formate+nadpox+h2o=co2tot+nadpred

-20.4151

1.4.1.1

alanine+nadox+h2o=pyruvate+nadred+monia

29.9682

.

Thermodynamics of Biochemical Reactions at Specified pH 1.4.1.2

glutamate+nadox+h2o=ketoglutarate+nadred+ammonia 38.7895

1.4.1.3

glutamate+nadpox+h2o=ketoglutarate+nadpred+amonia36.5242

1.4.1.10

glycine+nadox+h2o=glyoxylate+nadred+ammonia

51.8996

1.6.1.1

nadox+nadpred=nadred+nadpox

-0.891743

1.6.4.2

nadpox+2*glutathionered=nadpred+glutathioneox

6.01048

1.6.4.5

nadpox+2*thioredoxinred=nadpred+thioredoxinox

6.86709

2.3 .l.54

acetylcoA+fonnate=coA+pyruvate

11.0295

2.4.1.7

sucrose+pi=glucoselphos+fructose

-11.5121

2.4.1.8

maltose+pi=glucose+glucoselphos

-1.06837

2.4.2.1

adenosine+pi=adenine+riboselphos

27.5509

2.6.1.1

aspartate+ketoglutarate=oxaloacetate+glutamate

-1.47

2.6.1.2

alanine+ketoglutarate=pyruvate+glutarnate

-3.39595

2.6.1.35

glycine+oxaloacetate=glyoxylate+aspartate

9.94413

2.7.1.1

atp+glucose=adp+glucose6phos

-20.0611

2.7.1.23

atp+nadox=adp+nadpox

-8.32968

2.7.4.3

2*adp=arnp+atp

2.7092

3.1.3.1

amp+h2o=adenosine+pi

-12.9696

3 .l.3.lb

fructose6phos+h2o=fructose+pi

-13.6567

3 .l.3.lc

glucose6phos+h2o=glucose+pi

-11.6294

3.1.3.Id

glycerol3phos+h2o=glycerol+pi

1.78075

3.1.3.le

ppi+h20=2*pi

-23.15

3.2.1.3

maltose+h20=2*glucose

-19.92

3.2.1.23

lactose+h2o=glucose+galactose

-20.31

3.2.2.4

amp+h2o=adenine+ribose5phos

5.74391

3.2.2.7

adenosine+h2o=adenine+ribose

3.5668

3.5.1.2

glutamine+h2o=glutamate+ammonia

-12.7946

4.1.3.1

citrateiso=succinate+glyoxylate

-0.531653

4.1.3.6

citrate=acetate+oxaloacetate

3.2174

4.1.3.7

oxaloacetate+acetylcoA=citrate+coA

-45.0692

4.1.99.1

tryptophaneL+h2o=indole+pyruvate+ammonia

22.7596

4.2.1.2

fumarate+h2o=malate

-3.60654

4.2.1.3

citrate=aconitatecis+h20

8.42485

4.3.1.1

aspartate=fumarate+ammonia

12.2178

5.3.1.5

glucose=fructose

0.39

5.3.1.5b

xylose=xylulose

4.34

5.3.1.7

rnannose=fructose

-5.51

295

296

Mathernatica Solutions to Problerns 5.3.1.9

glucose6phos=fructose6phos

3.14096

5.3.1.15

lyxose=xylulose

2.99

5.3.1.20

ribose=ribulose

2.85

5.3.1.a

mannose=fructose

-5.51

5.4.2.2

glucoselphos=glucose6phos

-7.06836

5.4.2.7

riboselphos=ribose5phos

-8.08

6.2.1.1

atp+acetate+coA=amp+ppi+acetylcoA

-5.97683

6.3.1.2

atp+glutamate+ammonia=adp+pi+glutamine

-22.6469

6.4.1.1

atp+pyruvate+co2tot=adp+pi+oxaloacetate

-10.7687

(b) Make a table of the relevant data in the Goldberg and Tewari Tables. First make a vector of the experimental apparent equilibrium constants.

gHvector={7.0,7.8,6.8,7.1,6.5,7.0,6.9,8.05,7.92,7.8,6.2,7.3,7.5,7.97,6.9,7.~,6.4,7.5,6. 9,7.0,7.2,8.25,7.0,7.0,7.4,7.4,7.1,6.07,6.1,7.41,8.86,8.4,6.99,7.0,7.0,5.0,5.65,8.0,7.0 ,5.5,7.7,7.0,7.05,7.97,7.3,7.4,7~37,7~5,8.7,7.0,8.7,7.0,7.4,7.6,8.48,7.0,7.0,7.0,7.4~;

isvector={.25,.03,.05,.25,.05,.25,.25,.05,.1,.1,.07~.03~.1~.1~.24~~~~~~~~~ , . 1 , . 1 , . 1 , . 1 , . 5 , . 1 , . 1 , ~ 1 ~ . 0 4 ~ ~ 3 ~ ~ 2 4 ~ ~ 2 5 ~ ~ 1 ~ ~ 1 ~ ~ ,.1,.05,.3,.06,.04,.02,.1,.25,.25,.3,.02}

{0.25, 0.03, 0.05, 0.25, 0.05, 0.25, 0.25, 0.05, 0.1, 0.1, 0.07, 0.03, 0.1, 0.1, 0.24, ( 0.1, 0.1, 0.1, 0 . 5 , 0.1, 0.1, 0.1, 0.04, 0.3, 0.24, 0.25, 0.1, C.l, 0.01, 0.1, 0.1, 0. 0.1, 0.1, 0.1, 0.05, 0.3, 0.06, 0.04, 0.02, 0.1, 0.25, 0.25, 0.3, 0.02)

calcgvector=~glxlxlxl,glxlxlx26,glxlxlx27b,glxlxlx37.glxlxlx39, glxlxlx40,glxlxlx42,glxl x1x67,g1x1x1x79,glxlx99x7,g1x2x1x2,g1x2x1X10,g1x2x1x43,g1x4x1x1,g1~4x1x2,g1~4~1~3,g1~4~ lxlO,glx6xlxl,glx6x4x2, glx6x4x5,g2x3x1x54,g2x4x1x7 , g 2 ~ 4 ~ 1 x 8 , g 2 ~ 4 g2x6xlx1, ~ 2 ~ 1 , g2x6xlx2, g2~6~1~35,g2~7~1x1,g2x7xlx23,g2~7~4~3,g3xlx3xl,g3xlx3xlb,g3xl~3xlc,g3xlx3xld,g3xlx3xle, g3x2xlx3,g3x2xlx23,g3x2x2x4, g3x2x2x7,g3x5xlx2,g4xlx3x1,g4xlx3x6,g4xlx3x7, g 4 ~ 1 ~ 9 9 g4x2 ~1, ~ 1 x 2 g4x2xlx3, , glx3xlx1, g5x3xlx5,gSx3xlx5b,g5x3xlx7,g5x3xlx9,g5x3xlx15,g 5 ~ 3 ~ 1 ~ g2 50 ~, 3 ~ 1 x a , g 5 x 4 x 2 x 2 , g 5 x 4 x 2 x 7 , g 6 ~ 2 ~ l x l , g 6 ~ 3 ~ 1 ~ 2 tlA11,211 ~~6~4~1~~l {22.095, 38.896, 26.3652, 28.2639, 4.45812, 1.71088, -3.83041, 1.88013, 38.2358, -4.9221 38.7895, 36.5242, 51.8996, -0.891743, 6.01048, 6.86709, 11.0295, -11.5121, -1.06837, 2 -20.0611, -8.32968, 2.7092, -12.9696, -13.6567, -11.6294, 1.78075, -23.15, -19.92, -2C -0.531653, 3.2174, -45.0692, 22.7596, -3.60654, 8.42485, 12.2178, 0.39, 4.34, -5.51, ? -8.08, -5.97683, -22.6469, -10.7687)

Thermodynamics of Biochemical Reactions at Specified pH

297

roundCvec-,params-:E4,21l:=(*When a list of numbers ver has more digits to the r i g h t of the decimal point than you want, say 5, you can request 2 by using roundIvec,C5,2)1.*) Flatten [MapCNumberForm I#, params 1&, {vec 1, { 2 1 I I

calcgvec=round[calcgector,{S,2}] {22.1, 38.9, 26.37, 28.26, 4.46, 1.71, -3.83, 1.88, 38.24, -4.92, -15.14, -13.86, -20.4; 6.87, 11.03, -11.51, -1.07, 27.55, -1.47, -3.4, 9.94, -20.06, -8.33, 2.71, -12.97, -1: -20.31, 5.74, 3.57, -12.79, -0.53, 3.22, -45.07, 22.76, -3.61, 8.42, 12.22, 0.39, 4.34 -8.08, -5.98, -22.65, -10.77) ecnos=Ciil.l.l.lll, 111.1.1.26'1,1m1.1.1.27bii, "1.1.1.37ii,111.1.1.39ii,

m11.1.1.40ii, 111.1.1.42", \ "1.1.1.79","1.1.99.7","1.2",.1.2.1.10", " 1 . 2 . 1 . 4 3 " . "1.4.1 .1", "1. \ 4.1.2", "1.4.1- 3 " , "1.4.1. lo", " 1 . 6 . 1 . I", " 1 . 6 . 4 . 2 " . " 1 . 6 . 4 . 5 "," 2 . 3 . 1 . 5 4 " , " 2 . 4 . 1 . \ 7 1 1 , "2.4.1. a", " 2 . 4 . 2 . 1 " . " 2 . 6 . 1.I", " 2 . 6 . 1.2 " . " 2 . 6 . I. 35 81, " 2 . 7 1. I", '12.7.1.23 1 1 , " 2 . \ 7 . 4 . 3 " , " 3 . 1 . 3 . I", " 3 . 1 . 3 . 1b" ," 3 . 1 . 3 . 1 ~ " . " 3 . 1 . 3 . Id", " 3 . 1 . 3 . le", " 3 . 2 . 1 . 3 " , " 3 . 2 . 1 . \ 2 3'1, " 3 . 2 . 2 . 4 " , " 3 . 2 . 2 - I", " 3 . 5 . 1 . 2 " , " 4 . 1 . 3 . 1 " . " 4 . 1 . 3 . 6 " , " 4 . 1 . 3 . 7 " , "4.1.99.1", " 4 . \ 2 . 1 . 2 " . 114.2.1.3 " 4 . 3 . 1 . l l i , " 5 . 3 . 1 . S " , im5.3.1.5bi*, im5.3.1. 7 i ~ 5 . 3 . 1 . 9 1 ~", 5 . 3 . 1 . \ 15", " 5 . 3 . 1 . 2 0 " , " 5 . 3 . 1 .ana, " 5 . 4 . 2 . 2Ii, "5.4.2. I", " 6 . 2 . 1 . I", i i 6 . 3 . 1 . 2 " , i16.4.1.111 } ; "1.1.1.67",

.

TableForm~TransposeI~ecnos,rxvector,vector,~Hvector,~svector,gradevector1l,TableHeading s->{None, InEC NOS.^^, llReaction",llK1ln l'pH1r, "I", "Gr"11, Tablespacing-> { 1 , 1 ) 1 EC Nos.

1.1.1.1

React ion ethanol+nadox==acetaldehyde+nadred

K' pH 0.0000925 7.

I Gr 0.25 A

1 .l.1.26

glycolate+nadox=gloxylate+nadred

-7 1.03 10 7.8

0.03 B

1 .l.1.27b lactate+nadox=pyruvate+nadred

0.000017

6.8

0.05 A

1.1.1.37 malate+nadox=oxaloacetate+nadred

0.000012

7.1

0.25 A

1.1.1.39 malate+nadox+h2o=pyruvate+nadred+co2tot

0.00112

6.5

0.05 C

1.1.1.40 malate+nadpox+h2o=pyruvate+nadpred+co2tot

0.034

7.

0.25 A 0.25 A

1.1 .l.42

citrateiso+nadpox+h2o=ketoglutarate+nadpred+co2tot 0.72

6.9

1 .l.1.67

mannitolD+nadox=fructose+nadred

0.056

8.05 0.05 B

1 .l.1.79 glycolate+nadpox=glyoxylate+nadpred

-11 9. 10

7.92 0.1

B

1 .l.99.7 lactate+oxaloacetate=malate+pyruvate

4.3

7.8

0.1

B

420

6.2

0.07 D

1.2.1.10 acetaldehyde+coA+nadox=acetylcoA+nadred

2000

7.3

0.03 B

1.2.1.43 formate+nadpox+h2o=co2tot+nadpred

650.

7.5

0.1

c B

1.2.1.2

formate+nadox+h2o=co2tot+nadred

3 1.4.1.1

alanine+nadox+h2o=pyruvate+nadred+amonia

500000

7.97 0.1

1.4.1.2

glutamate+nadox+h2o=ketoglutarate+nadred+ammonia

-6 1.5 10

6.9

0.24 A

1.4.1.3

-6 glutamate+nadpox+h2o=ketoglutarate+nadpred+a.mmonia1.2 10

7.

0.47 A

0.000057

6.4

0.08

C

B

1.4.1.10 glycine+nadox+h2o=glyoxylate+nadred+ammonia 1.6.1.1

nadox+nadpred=nadred+nadpox

1.41

7.5

0.1

1.6.4.2

nadpox+2*glutathionered=nadpred+glutathioneox

0.0156

6.9

0.25 A

298

Mathematica Solutions to Problems

c

1.6.4.5

nadpox+2*thioredoxinred=nadpred+thioredoxinox

0.036

7.

0.1

2.3.1.54

acetylcoA+formate=coA+pyruvate

23

7.2

0.05 C

2.4.1.7

sucrose+pi=glucoselphos+fructose

31.5

8.25 0.1

A

2.4.1.8

maltose+pi=glucose+glucoselphos

0.23

7.

0.1

c

2.4.2.1

adenosine+pi=adenine+riboselphos

0.00541

7.

0.1

B

2.6.1.1

aspartate+ketoglutarate=oxaloacetate+glutamate

0.148

7.4

0.1 A

2.6.1.2

alanine+ketoglutarate=pyruvate+glutamate

0.658

7 . 4 0.5 A

2.6.1.35

glycine+oxaloacetate=glyoxylate+aspartate

0.016

7.1

2.7.1.1

atp+glucose=adp+glucose6phos

294

6.07 0.1 A

29.3

6.1

2.7.1.23 atp+nadox=adp+nadpox

0.1 B 0.1

B

2.7.4.3

2*adp=amp+atp

0.365

7.41 0.04 A

3.1.3.1

amp+h2o=adenosine+pi

189

8.86 0.3 A

3.1.3.lb

fructose6phos+h2o=fructose+pi

262

8.4

3.1.3.lc

glucose6phos+h2o=glucose+pi

110

6.99 0.25 A

3.1.3.Id

glycerol3phos+h2o=glycerol+pi

68

7.

0.1

B

3.1.3.le

ppi+h20=2*pi

20000

7.

0.1

B

3.2.1.3

maltose+h20=2*glucose

200

5.

0.01

3.2.1.23

lactose+h2o=glucose+galactose

35.2

5.65 0.1

A

3.2.2.4

amp+h2o=adenine+ribose5phos

170

8.

0.1

B

3.2.2.7

adenosine+h2o=adenine+ribose

53

7.

0.1

B

3.5.1.2

glutamine+h2o=glutamate+ammonia

896

5.5

0.1

B

4.1.3.1

citrateiso=succinate+glyoxylate

0.0023

7.7

0.1 B

4.1.3.6

citrate=acetate+oxaloacetate

0.877

7.

0.02 A

4.1.3.7

oxaloacetate+acetylcoA=citrate+coA

6 1.14 10

7.05 0.25 A

4.1.99.1

tryptophaneL+h2o=indole+pyruvate+aonia

0.00022

7.97 0.1 A

4.2.1.2

fumarate+h2o=malate

4.87

7.3

0.1 A

4.2.1.3

citrate=aconitatecis+h20

0.032

7.4

0.1

4.3.1.1

aspartate=fumarate+ammonia

0.00471

7.37 0.1 A

5.3.1.5

glucose=fructose

0.87

7.5

0.1

A

0.172

8.7

0.1

A

5.3.1.5b xylose=xylulose

0.24 A

c

A

5.3.1.7

mannose=fructose

3.

7.

0.05 B

5.3.1.9

glucose6phos=fructose6phos

0.299

8.7

0.3

5.3.1.15

lyxose=xylulose

0.23

7.

0.06 B

0.391

7 . 4 0.04 A

1.5

7.6

5.3.1.20 ribose=ribulose 5.3.1.a

mannose=fructose

A

0.02 B

299

Thermodynamics of Biochemical Reactions at Specified pH 5.4.2.2

glucoselphos=glucose6phos

17.1

8.48 U . 1

5.4.2.7

riboselphos=ribose5phos

26

7.

0.25 A

6.2.1.1

atp+acetate+coA=amp+ppi+acetylcoA

11.1

7.

0.25 A

6.3.1.2

atp+glutamate+ammonia=adp+pi+glutamine

270

7.

0.3 A

6.4.1.1

atp+pyruvate+co2tot=adp+pi+oxaloacetate

6.55

7.4 0.02 A

A

The references are given in Goldberg and Tewari.

(c) Make a table of the differences between the values of the standard transformed Gibbs energies of reaction calculated in part (a) at pH 7 and the experimental values in Goldberg and Tewari. Calculate the experimental standard transformed Gibbs energies of reaction. gprime=-8.31451*.29815*Log[vectorl

{23.0254, 39.883, 27.2248, 28.0882, 16.8432, 8.38238, 0.814352, 7.1454, 57.3416, -3.615E 33.2431, 33.7963, 24.2256, -0.851749, 10.3137, 8.24069, -7.7728, -8.55242, 3.64328, 1; -8.37294, 2.49845, -12.9941, -13.8038, -11.6524, -10.46, -24.5505, -13.1344, -8.82773, 0.325361, -34.5731, 20.8776, -3.92444, 8.53267, 13.2825, 0.345227, 4.36364, -2.72343, -7.03799, -8.07673, -5.96675, -13.8783, -4.65914) gprimer=round [gprime,{ 5,2 1 1

(23.03, 39.88, 27.22, 28.09, 16.84, 8.38, 0.81, 7.15, 57.34, -3.62, -14.97, -18.84, -16. 10.31, 8.24, -7.77, -8.55, 3.64, 12.94, 4.74, 1.04, 10.25, -14.09, -8.37, 2.5, -12.99, -8.83, -12.73, -9.84, -16.85, 15.06, 0.33, -34.57, 20.88, -3.92, 8.53, 13.28, 0.35, 4. -7.04, -8.08, -5.97, -13.88, -4.66)

Calculate differences before rounding. diff=calcgvector-gprime

{-0.930416, -0.986987, -0.859612, 0.175639, -12.3851, -6.6715, -4.64476, -5.26526, -19.1 -4.35884, 0.161716, 5.54638, 2.72787, 27.6739, -0.039994, -4.30324, -1.3736, 18.8023, -4.43352, -0.30683, -5.97168, 0.0432646, 0.210751, 0.0244942, 0.147033, 0.0229674, 12. 18.4754, 13.409, 4.05733, -15.591, 2.89204, -10.4961, 1.882, 0.317903, -0.107815, -1.c 0.148067, -0.653284, 0.522128, -4.50486, -0.0303697, -0.00327266, -0.0100851, -8.7685: dif =round [diff, { 6,2 11

{-0.93, -0.99, -0.86, 0.18, -12.39, -6.67, -4.64, -5.27, -19.11, -1.31, -0.17, 4.98, -4. -1.37, 18.8, -2.96, -4.71, 14.61, -6.21, -4.43, -0.31, -5.97, 0.04, 0.21, 0.02, 0.15, 13.41, 4.06, -15.59, 2.89, -10.5, 1.88, 0.32, -0.11, -1.06, 0.04, -0.02, -2.79, 0.15, -8.77, -6.11}

Calculate the differences.and make a table. TableForm[Transpose[{ecnos,rxvector,calcgvec,gprimer,dif}],TableHead~ngs-~iNone,i"EC Nos.", 18Reaction", "Calc", Wxptl1I,'Calc-Exptl") 1 ,TableSpacing->{l,111 Calc 22.1

Exptl Calc-Exptl 23.03 -0.93

1.1.1.26 glycolate+nadox=gloxylate+nadred

38.9

39.88

-0.99

1.1.1.27b lactate+nadox=pyruvate+nadred

26.37

27.22

-0.86

EC Nos. 1.1.1.1

Reaction

ethanol+nadox==acetaldehyde+nadred

300

Mathematica Solutions to Problems 1.1.1.37 malate+nadox=oxaloacetate+nadred

28.26

28.09

0.18

1.1.1.39 malate+nadox+h2o=pyruvate+nadred+co2tot

4.46

16.84

-12.39

1 .l.1.40 rnalate+nadpox+h2o=pyruvate+nadpred+co2tot

1.71

8.38

-6.67

0.81

-4.64

1.88

7.15

-5.27

57.34

-19.11

1 .l.1.42

citrateiso+nadpox+h2o=ketoglutarate+nadpred+co2tot-3.83

1.1.1.67 mannitolD+nadox=fructose+nadred 1.1.1.79

glycolate+nadpox=glyoxylate+nadpred

38.24

1 .l.99.7

lactate+oxaloacetate=malate+pyruvate

--4.92 -3.62

1.2.1.2

formate+nadox+h2o=co2tot+nadred

-15.14 -14.97 -0.17

1.2.1.10

acetaldehyde+coA+nadox=acetylcoA+nadred

-13.86 -18.84 4.98

1.2.1.43

formate+nadpox+h2o=co2tot+nadpred

-20.42 -16.06 -4.36

1.4.1.1

alanine+nadox+h2o=pyruvate+nadred+amonia

29.97

29.81

0.16

1.4.1.2

glutamate+nadox+h2o=ketoglutarate+nadred+amonia 38.79

33.24

5.55

1.4.1.3

glutamate+nadpox+h2o=ketoglutarate+nadpred+ammonia36.52

33.8

2.73

1.4.1.10

glycine+nadox+h2o=glyoxylate+nadred+ammonia

51.9

24.23

27.67

1.6.1.1

nadox+nadpred=nadred+nadpox

-0.89

-0.85

-0.04

1.6.4.2

nadpox+2*glutathionered=nadpred+glutathioneox

6.01

10.31

-4.3

1.6.4.5

nadpox+2*thioredoxinred=nadpred+thioredoxinox

6.87

8.24

-1.37

2.3.1.54

acetylcoA+formate=coA+pyruvate

11.03

-7.77

18.8

2.4.1.7

sucrose+pi=glucoselphos+fructose

-11.51 -8.55

-2.96

2.4.1.8

maltose+pi=glucose+glucoselphos

-1.07

3.64

-4.71

2.4.2.1

adenosine+pi=adenine+riboselphos

27.55

12.94

14.61

2.6.1.1

aspartate+ketoglutarate=oxaloacetate+glutamate

-1.47 4.74

-6.21

2.6.1.2

alanine+ketoglutarate=pyruvate+glutamate

--3.4

1.04

-4.43

2.6.1.35

glycine+oxaloacetate=glyoxylate+aspartate

9.94

10.25

-0.31

2.7.1.1

atp+glucose=adp+glucose6phos

-20.06 -14.09 -5.97

2.7.1.23

atp+nadox=adp+nadpox

-8.33

-8.37

0.04

2.7.4.3

2*adp=amp+atp

2.71

2.5

0.21

3.1.3.1

amp+h2o=adenosine+pi

--12.97-12.99 0.02

3.1.3.lb

fructose6phos+h2o=fructose+pi

-13.66 -13.8

3.1.3.lc

glucose6phos+h2o=glucose+pi

-11.63 -11.65 0.02

3.1.3.ld glycerol3phos+h2o=glycerol+pi

1.78

-1.31

0.15

-10.46 12.24

3.1.3.le

ppi+h20=2*pi

-23.15 -24.55 1.4

3.2.1.3

maltose+h20=2*glucose

-19.92 -13.13 -6.79

3.2.1.23

lactose+h2o=glucose+galactose

-20.31 -8.83

3.2.2.4

amp+h2o=adenine+ribose5phos

5.74

-12.73 18.48

3.2.2.7

adenosine+h2o=adenine+ribose

3.57

-9.84

-11.48 13.41

Thermodynamics of Biochemical Reactions at Specified pH

301

3.5.1.2

glutamine+h2o=glutamate+ammonia

-12.79 -16.85 4.06

4.1.3.1

citrateiso=succinate+glyoxylate

-0.53 15.06 -15.59

4.1.3.6

citrate=acetate+oxaloacetate

3.22

4.1.3.7

oxaloacetate+acetylcoA=citrate+coA

-45.07 -34.57 -10.5

4 .l.99.1

tryptophaneL+h2o=indole+pyruvate+aonia

22.76

20.88

4.2.1.2

fumarate+h2o=malate

-3.61

-3.92 0.32

4.2.1.3

citrate=aconitatecis+h20

8.42

8.53

-0.11

4.3.1.1

aspartate=fumarate+ammonia

12.22

13.28

-1.06

5.3.1.5

glucose=fructose

0.39

0.35

0.04

5.3.1.5b

xylose=xylulose

4.34

4.36

-0.02

5.3.1.1

mannose=fructose

-5.51 -2.72 -2.79

5.3.1.9

glucosebphos=fructosebphos

3.14

2.59

0.15

5.3.1.15

lyxose=xylulose

2.99

3.64

-0.65

5.3.1.20

ribose=ribulose

2.85

2.33

0.52

5.3.1.a

mannose=fructose

-5.51 -1.01 -4.5

5.4.2.2

glucoselphos=glucose6phos

-7.07 -7.04 -0.03

5.4.2.1

riboselphos=ribose5phos

-8.08

-8.08

-0.00

6.2.1.1

atp+acetate+coA=amp+ppi+acetylcoA

-5.98 -5.91

-0.01

6.3.1.2

atp+glutamate+ammonia=adp+pi+glutamine

-22.65 -13.88 -8.77

6.4.1.1

atp+pyruvate+co2tot=adp+pi+oxaloacetate

-10.77 -4.66

0.33

2.85 1.88

-6.11

There are problems with adenine, glyolate, glyoxylate,,and glycerol3phos, which indicates that their values should be recalculated or should be calculated from other reactions. Since most of the species properties in BasicBiochemData2 can be obtained by several different paths, it is possible to find and correct errors.

4,s Calculate the standard transformed reaction Gibbs energies, appparent equilibrium constants, and changes in the binding of hydrogen ions for the ten reactions of glycolysis at 298,15 K, pHs 5 , 6 , 7, 8, and 9 and ionic strengths of .O, 0.10, and 0.25 M. Also calculate these properties for the net reaction.. (BasicBiochemData2 has to be loaded) calcNHrx[eC, pHlist-, change in the binding ionic strengths.*) energy = Solve[eq, D[energy[[l,l,2]1, pH -> pHlist / .

islist-] := Module[{energy},(*This program calculates the of hydrogen ions in a biochemical reaaction at specified gHs and deli pH1/(8.31451*0.29815*Log[lOl) / . is -> islist]

rxthermotab[eC, pHlist-, islist-] := Module[{energy, tg, tk, tn}, (*This program uses three other programs to make a thermodynamic table of standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the number of hydrogen ions bound in a biochemical reaction.*) t g = calctrGerx[eq, pHlist, islist]; t k = calckprime[eq, pHlist, islist]; tn = calcNHrx[eq, pHlist, islist]; TableForm[Join[ {tg, tk, tn)] ] ]

302

Mathematica Solutions to Problems

Reaction 1

-37.3892 -36.2155 -35.8228

-19.9564 -18.0757 -17.4137

-21.1455 -19.82 -19.4683

-24.8972 -24.6736 -24.4199

-31.3157 -30.4846 -30.1133

3134.61

5064.24

23002.6

306367.

1467.94

2966.78

21018.9

219099.

1123.89

2574.39

18973.7

188625.

6 3.55032 10 6 2.21129 10 6 1.88735 10

-0.177235 -0.122329 -0.139449

-0.336077 -0.579942 -0.649491

-0.992429 -1.01164 -0.984363

-1.12833 -1.00952 -1.0005

-1.02082 -1.0011 -1.00008

This program produces three tables. The top table gives the standard transformed reaction Gibbs energies at three ionic strengths and five pH values. The second table gives the corresponding equilibrium constants, and the third table gives the changes in the binding of hydrogen ions. Reaction 2

3.9532 3.89797 3.86839

3.72567 3.5248 3.45934

3.2948 3.20516 3.18839

3.15854 3.147 3.1451

3.14189 3.14071 3.14051

0.202971 0.207543 0.210035

0.222482 0.24126 0.247715

0.264715 0.274463 0.276326

0.279673 0.280978 0.281193

0.281558 0.281693 0.281714

-0.0141959 -0.0330731 -0.0419873

-0.0733161 -0.0847485 -0.080239

-0.0509985 -0.0242531 -0.0183996

-0.00731544 -0.00280164 -0.00204602

-0.000761426 -0.000284407 -0.000206853

Reaction 3

-12.5514 -12.258 -12.3548

-13,7161 -15.6976 -16.9525

-17.4527 -21.884 -23.2451

-23.8749 -27.9151 -29.1287

-29.9491 -33.6694 -34.858

158.085 140.444

252.901 562.446

1141.72 6821.56

15229.1 77710.5

176534. 791752.

146.033

933.1

11812.6

126794.

6 1.27886 10

-0.175363 -0.260983 -0.410005

-0.330035 -0.95943 -1.08946

-0.993053 -1.10486 -1.06644

-1.12864 -1.01996 -1.00934

-1.02085 -1.00216 -1.00097

Reaction 4 rxthermntab[fructosel6~hos+de==dihydroxyacetonephos+glyceraldehydeghos,~5,6,7,8,9},{O,. 1, -2511

Thermodynamics of Biochemical Reactions at Specified pH 23.2659 23.9815 24.3294

20.3466 22.0132 23.1829

17.2974 21.4975 23.0316

16.6248 21.4426 23.0188

16.5486 21.4371 23.0175

0.0000839493 0.0000629003 0.000054664

0.000272551 0.000139146 0.0000868079

0.0009325 0.000171327 0.0000922697

0.00122317 0.000175161 0.0000927491

0.00126134 0.00017555 0.0000927959

-0.246757 -0.340222 -0.289279

-0.714037 -0.211319 -0.0732304

-0.269856 -0.024558 -0.00589343

-0.0337308 -0.00246096 -0.000561605

-0.00345608 -0.000246092 -0.0000558653

Reaction 5

7.66 7.66 7.66

7.66 7.66 7.66

7.66 7.66 7.66

7.66 7.66 7.66

7.66 7.66 7.66

0.0455023 0.0455023 0.0455023

0.0455023 0.0455023 0.0455023

0.0455023 0.0455023 0.0455023

0.0455023 0.0455023 0.0455023

0.0455023 0.0455023 0.0455023

-14 2.36514 10 -14 5.35268 10 -14 5.66389 10

-14 2.48962 10 -15 6.22405 10 -14 1.24481 10

-15 1.86721 10 -15 3.11202 10 -15 1.24481 10

-15 1.24481 10 -15 1.24481 10 -16 -6.22405 10

-16 6.22405 10 -15 1.24481 10 -16 -6.22405 10

Reaction 6

22.8921 16.1673 14.0984

13.849 8.4353 6.71564

8.05124 3.1141 1.21649

4.32833 -1.94228 -4.21929

-0.337223 -7.5227 -9.88359

0.0000976101 0.00147106 0.00338903

0.00374781 0.0332818 0.0666004

0.038859 0.284732 0.612183

0.174467 2.18912 5.48509

1.14572 20.7928 53.8916

-1.82897 -1.64339 -1.569

-1.28797 -1.09084 -1.06683

-0.769332 -0.840272 -0.921309

-0.669347 -0.947342 -0.981391

-0.933047 -0.993787 -0.997935

Reaction 7

-8.77058 -8.35908 -8.31749

-8.3272 -8.21794 -8.22167

-8.00276 -8.11648 -8.22407

-7.96743 -8.30786 -8.34411

-8.29556 -8.36297 -8.36722

34.3977 29.1366 28.6519

28.7643 27.5241 27.5655

25.2357 26.4203 27.5922

24.8786 28.5408 28.9611

28.3995 29.1824 29.2325

0.13882 0.0248626 0.0107016

0.0431119 0.0334161 0.0225207

0.0716595 -0.0229746 -0.0271383

-0.0704186 -0.0217609 -0.00964887

-0.0275038 -0.00279498 -0.00111155

Reaction 8

303

304

Mathematica Solutions to Problems 5.53164 5.53714 5.54145

5.54601 5.5948 5.62832

5.66019 5.86614 5.9385

5.98488 6.10926 6.12755

6.13662 6.15453 6.1566

0.107375 0.107137 0.106951

0.106755 0.104674 0.103268

0.101949 0.0938216 0.0911224

0.0894334 0.0850572 0.0844318

0.0841235 0.0835179 0.0834482

0.00065925 0.00284928 0.00453314

0.0062929 0.0234401 0.0334474

0.0416282 0.0631637 0.0578654

0.0509505 0.0188138 0.0124135

0.00908086 0.00218857 0.00136563

Reaction 9 rxthermotab[pg2+de==pep+h2o,~5,6,7,8,9~,~0,.1,.25~1

-0.828959 -0.891715 -0.939757

-0.989798 -1.47469 -1,76463

-2.0152 -3.25948 -3.59868

-3.7985 -4.28122 -4.34674

-4.37876 -4.44115 -4.44829

1.3971 1.43292 1.46096

1.49075 1.81281 2.03774

2.25448 3.7242 4.27029

4.62877 5.62385 5.77446

5.84954 5.99863 6.01593

-0.00760123 -0.0321025 -0.0501811

-0.0683949 -0.213665 -0.274923

-0.313273 -0.312677 -0.257218

-0.212886 -0.0680294 -0.0440393

-0.0319192 -0.00755601 -0.0047052

Reaction 10 rxthermotab[pep+adg+de==pyruvate+atp,{5,6,7,8,9},~0,.1,.25}1

-33.4613 -34.1841 -34.4724

-32.7661 -33.1449 -33.1063

-30.6224 -29.2617 -28.8451

-25.1722 -23.6955 -23.2908

-19.2526 -17.993 -17.5968

728017. 974465,

6 1.09465 10

549974. 540772.

231625. 133784.

25700.8 14166.3

2359.9 1419.79

630867.

113085.

12032.5

1210.04

0.150557 0.0719355 0.0826948

0.151752 0.38045 0.480624

0.700597 0.915575 0.927296

1.06297 0.99698 0.993667

1.01353 0.999809 0.999384

Net Reaction rxthermotab[glucose+2*pi+2*adp+2*nadox+de==2*pyruvate+2*atp+2*nadred+2*h20,~5,6,7,8,9~, { O r -1,-2511

-48.5056 -59.9344 -63.6158

-67.9556 -77.5099 -80.8106

-80.9971 -90.3854 -93.5651

-92.2429 -101.978 -105.141

6 5.03504 10 7 2.36512 10

8 3.1461 10 10 3.16219 10 11 1.39618 10

11 8.0398 10 13 3.79375 10 14 1.43657 10

14 1.54878 10 15 6.83502 10 16 2.46488 10

16 1.44602 10 17 7.3388 10 18 2.62942 10

-3.70662 -3.90829 -3.92322

-3.76388 -3.56983 -3.50274

-2.84378 -2.55969 -2.5161

-1.97548 -2.07742 -2.07045

-1.98561 -2.00807 -2.00732

-26.9029 -38.2553 -42.0903 51659.7

4.9 Calculate the standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the binding of hydrogen ions for the four reactions of gluconeogenesis that are different from those in glycolysis at 298.15 K, pHs 5 , 6,

Thermodynamics of Biochemical Reactions at Specified pH

305

7, 8, and 9 and ionic strengths 0, 0.10, and 0.25 M. Also calculate the properties of the net of pyruvate carboxylase and phosphoenolpyruvate carboxykinase reactions and the net reaction of gluconeogenesis. (BasicBiochemData2 must be loaded) pyruvate carboxylase reaction TableForm[Transpose[calctrGerx[pyruvate+co2tot+atp+de==oxaloacetate+adp+p~,{5,6,7,8,9~, {0,.1,.25}]],TableHeading~->{{~~I = 0 Mml,mlI = 0.10 M","I = 0.25 M"}.{rlgH 5","pH 6","pH 7","pH 8 m m , 1 1 p9"}}1 H

I = O M

PH 5 1.16519

PH 6 -4.37511

PH 7 -8.52558

PH 8 -13.8718

PH 9 -19.6143

I = 0.10 M

0.785196

-4.34584

-8.83247

-14.077

-19.4656

I = 0.25 M

0.754643

-4.31006

-8.8077

-14.0617

-19.3633

TableForm[Transpose[calckpr~e[pyruvate+co2tot+at~+de==oxaloacetate+ad~+~~,{5,6,7,8,9~, {0,.1,.25}]].TableHeadings-,{{~~I= 0 M","I = 0 . 1 0 M",llI = 0.25 M"},{"pH 5","pH 6","pH 7 " , " p H 8 " , 1 1 p H 91t}}J I = O M

PH 5 -3.00283

PH 6 1.22754

PH 7 1.54323

PH 8 -3.45614

PH 9 -9.42638

I = 0.10 M

0.103784

3.61904

1.59418

-3.70581

-9.63967

I = 0.25 M

1.15447

4.19971

1.61744

-3.72164

-9,74206

TableForm[Transpose[calck~ri~e[oxaloacetate+atp+h2o+de==pep+adp+co2tot,~5,6,7,8,9~,~~,. 1,.25}]],TableHeading~->{{~~I= 0 M","I = 0 . 1 0 M1m,"I = 0.25 Mml},{"pH 5","pH 6","pH 7 " , 1 m p H 8 1 1 , " p H 9"))l

PH 5

3.35791

PH 6 0.609461

PH 7 0.536586

PH 8 4.03168

PH 9 44.8148

I = 0.10 M

0.958999

0.23226

0.525671

4.45889

48.8413

I = 0.25 M

0.627693

0.183758

0.520761

4.48745

50.901

I = O M

306

Mathematica Solutions to Problems TableForm[(1/(8.31451*.29815*Log[lO] ))*D[~pep+ad~+co2tot-oxaloacetate-at~-h2o~,gHl/.~s>(O, .l, . 2 5 ) / . p H - > { 5 , 6 , 7 , 8 , 9 ) , T a b l e H e a d i n g s - > E E " I = 0 M","I = 0.10 M " , " I = 0.25 M1l),{"gH 5 " , 1 1 p H 6","pH 7","pH 8","pH 9"))l

I = O M

PH 5 0.808208

PH 6 0.547488

PH 7 -0.512396

PH 8 -1.04491

PH 9 -1.05597

I = 0.10 M

0.862233

0.206083

-0.792542

-0.99541

-1.11014

I = 0.25 M

0.840963

0.0667518

-0.82107

-0.998722

-1.1457

Net of the preceding two reactions

TableForm[Transpose[calctrGerx[pyruvate+2*atp+h2o+de==gep+2*adg+p~,~~,6,7,8,9~,~~,.1,.~ S)]] ,TableHeadings->(("I = 0 M","X = 0.10 M","I = 0 . 2 5 M"),{"gH 5","gH 6","gH 7","pH 8 m 1 , 1 * p H9n1})1

I = O M

PH 5 -1.83764

PH 6 -3.14757

PH 7 -6.98235

PH 8 -17.328

PH 9 -29.0407

I = 0.10 M

0.88898

-0.726795

-7.23829

-17.7828

-29.1052

I = 0.25 M

1.90911

-0.110354

-7.19026

-17.7833

-29.1054

TableForm[Transpose[calck~rime[gyruvate+2*atp+h2o+de==gep+2*adg+p~,~5,6,7,8,9~,iO,.l,.~ 5}]],TableHeading~->{i~~I = 0 MI1,"I = 0.10 M","I = 0 . 2 5 M1l),{"gH 5","gH 6","pH 7","gH 811,11pH9m1))1 I = O M

PH 5 2.09864

PH 6 3.55982

PH 7 16.7204

PH 8 1085.7.1

PH 9 122370.

I = 0.10 M

0.698648

1.34069

18.539

1304.37

125599.

I = 0.25 M

0.462956

1.04552

18.1833

1304.63

125606.

TableForm[(1/(8.31451*.29815*Log[10]))*D[(pep+2*adp+~i-gyruvate-2*at~-h~o~,gHl/.is>~0,.1,.25)/.gH->{5,6,7,8,9),TableHeadings->{i1'I = 0 M","I = 0.10 M","I = 0 . 2 5 MI' 1, ("pH 5", "pH 6", "pH 7 'I, "pH 8", "pH 9") 11

I = O M

PH 5 -0.297246

PH 6 -0.269812

PH 7

-1.27871

PH 8 -2.07523

PH 9 -2.02073

I = 0.10 M

-0.11779

-0.595535

-1.63573

-1.95827

--1.99578

I = 0.25 M

-0.121086

-0.729254

-1.66925

-1.95844

-1.99572

Fructose I ,6-biphosphatase TableFo~[Trans~ose[calctrGerx[f~ctosel6ghos+h2o+de==fructose6phos+p~,i5,6,7,8,9~,iO,. 1,.25)]],TableHeadings->{{"I = 0 Mmm,llI = 0.10 M","I = 0 . 2 5 M"),I"gH 5","gH 6","gH 7 " , 9 S i 81n,11pH 91))] I = O M

PH 5 -22.7476

PH 6 -22.1975

PH 7 -20.1521

PH 8 -18.6253

PH 9 -18.3442

I = 0.10 M

-21.0371

-18.1741

-14.6161

-13.5633

-13.4289

I

-20.2085

-16.2642

-12.7902

-11.9455

-11.8441

=

0.25 M

TableForm[Trans~ose[calck~rime[f~ctosel6ghos+h2o+de==f~ctose6phos+g~,i5,6,7,8,9~,~O, 1,.25)1],TableHeading~->{{*~I= 0 M S 1 , l 1 I = 0.10 M","I = 0 . 2 5 M " ) , { ' l p H 5","gH 6","pH 7","pH 8","pH 9"))]

Thermodynamics of Biochemical Reactions at Specified pH

I = O M

PH 5 9664.7

PH 6 7741.4

PH 7 3392.13

PH 8 1832.26

PH 9 1635.84

I = 0.10 M

4847.55

1527.39

363.586

237.781

225.229

I = 0.25 M

3470.27

706.875

174.073

123.807

118.847

307

TableForm~(1/(8.3145l*.298l5*Log[lO]))*D[(f~ctose6phos+pi-f~ctosel6phos-h2o~,~Hl/.is>{0,.1,.25)/.pH->{5,6,7,8,9},TableHeadingS->{{~'I = 0 M","I = 0.10 M","I = 0.25 Mml),{llpH 51*,"pH6","pH 7 1 1 , * t p H 8ms,11pH 9t1)>1

I = O M

PH 5 0.028674

PH 6 0.211976

PH 7 0.414941

PH 8 0.11638

PH 9 0.0136539

I = 0.10 M

0.215128

0.744345

0.384706

0.0586725

0.00618982

I = 0.25 M

0.371614

0.840829

0.324487

0.0445667

0.00463044

Glucose 6-phosphatasephosphatase TableForm[Transpose[calctrGerx[glucose6phos+h2o+de==glucose+~~,~5,6,7,8,9?,~O,.l,.25~l~ ,TableHeadings->{{"I = 0 M 1 m r " I = 0.10 M","I = 0.25 M"},{8mpH 5","pH 6","pH 7","pH 8","pH 9"))I

I = O M

PH 5 -15.3426

PH 6 -14.7682

PH 7 -12.7076

PH 8 -11.1844

PH 9 -10.9041

I = 0.10 M

-15.2194

-14.0517

-11.8264

-10.9938

-10.8828

I = 0.25 M

-15.1497

-13.7484

-11.6155

-10.9608

-10.8793

TableForm~Transpose[calckprime[glucose6phos+h2o+de==glucose+~~,~5,6,7,8,9~,~O,.l,.25~ll ,TableHeadings->{{"I = 0 M1t,mlI = 0.10 Mn,"I = 0.25 M"},{"gH 5","pH 6","pH 7","pH 8","pH 9"))l

I = O M

PH 5 487.412

PH 6 386.594

PH 7 168.366

PH 8 91.0791

PH 9 81.3396

I = 0.10 M

463.784

289.565

118.

84.3364

80.6433

I = 0.25 M

450.911

256.21

108.375

83.2229

80.5302

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[~glucose+pi-glucose6phos-h2o~,pHl/.~s>{0,.1,.25)/.gH->{5,6,7,8,9},TableHeadings->{{11I = 0 M1l,ltI = 0.10 M","I = 0.25 M"},{"pH 5 1 m , " p H 6","pH 7","pH 8","pH 9"1}1 I = O M

PH 5 0.0305457

PH 6 0.218017

PH 7 0.414317

PH 8 0.116071

PH 9 0.013619

I = 0.10 M

0.0764751

0.364857

0.291488

0.0482304

0.00513333

I = 0.25 M

0.101058

0.400861

0.242412

0.035721

0.00373907

Net reaction for gluconeogenesis

TableForm[Tr~spose[calctrGerx[2*~y~vate+6*atp+2*nadred+6*h2o+de==glucose+6*ad~+6*p~+ *nadox, {5,6,7,8,9), ( 0 , .l, .25}11 .TableHeading~->{{~~I = 0 M","I = 0.10 M","I = 0.25 M" ) ,{ "pH 5 , pH 6","pH 7","pH 8","pH 9"))l

I = O M

PH 5 -114.293

PH 6 -95.1491

PH 7 -82.4634

PH 8 -89.0035

PH 9 -100.93

I = 0.10 M

-94.9253

-75.5524

-68.4902

-75.5282

-86.4153

I = 0.25 M

-88.163

-69.2508

-63.3307

-70.7316

-81.6672

308

Mathematica Solutions to Problems

TableForm[Trans~ose[calckprime[2*pyruvate+6*atp+2*nadred+6*h2o+de==glucose+6*adp+6*p~+2 *nadox, {5,6,7,8,9), (0, -1,.25) 1 1 ,TableHeadings->{{"I = 0 M", "I = 0.10 M", "I = 0.25 M"},{"pH 511,1tpH 6","pH 7","pH 8","pH 9"))l

PH 5

20

PH 6

PH 7

PH 8

PH 9

16 4.66988 10

14 2.79825 10

15 3.91429 10

17 4.80954 10

I = O M

1.05479 1 0

I = 0.10 M

16 4.26674 10

13 1.72242 10

11 9.97467 10

13 1.70563 10

15 1.37793 10

I

15 2.78871 10

12 1.35564 10

11 1.24448 10

12 2.46364 10

14 2.02949 10

=

0.25 M

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(glucose+6*adp+6*~i+2*nadox-2*py~vate-6*atp-2 *nadred-6*h2o),gH]/.is->{O,.l,.25}/.pH->{5,6,7,8,9},TableHeadings-~{{"I = 0 M","I = 0.10 ~ 1 1 , 1 9 1 = 0.25 M"},{"pH 511,11pH 611,"pH7","pH 8","pH 9")>1

I = O M

PH 5 3.11986

PH 6 3.29164

PH 7 0.531329

PH 8 -2.07356

PH 9 -2.04318

I = 0.10 M

3.72487

2.70949

-0.320941

-1.76774

-1.9758

I = 0.25 M

3.16965

2.50822

-0.451703

-1.78866

-1.97804

4.10 Calculate the standard transformed reaction Gibbs energies, apparent equilibrium constants, and changes in the binding of hydrogen ions for the pyruvate dehydrogenase reaction and the nine reactions of the citric acid cycle at 298.15 K, pHs 5 , 6, 7, 8, and 9 and ionic strengths 0, 0.10, and 0.25 M. Also calculate these properties for the net reaction of the citric acid cycle, the net reaction for pyruvate dehydrogenase plus the citric acid cycle, and the net reaction for glycolysis, pyruvate dehydrogenase, and the citric acid cycle.

(BasicBiochemData2 must be loaded) Pyruvate dehydrogenase TableForm[Transpose[calctrGerxCpyruvate+coA+nadox+h2o+de==co2tot+acetylcoA+nadred, {5,6, 7,8,9),{0, .l, .25)]] ,Tab1eHeadings->{C1*I= 0 Mml,"I= 0.10 M a n r m =m I0.25 M"), {"pH 5","pH 6i1,iipH 71i,ripH 811,11pH 9"))l

I = O M

PH 5 -23.6334

PH 6 -24.4065

PH 7 -27.5641

PH 8 -32.0578

PH 9 -34.6066

I = 0.10 M

-24.9212

-26.0596

-29.7622

-34.0761

-36.2027

I = 0.25 M

-25.3442

-26.6231

-30.4807

-34.7047

-36.7463

TableForm[Transpose[calckprime[~yruvate+coA+nadox+h2o+de==co2tot+acetylcoA+nadred,~5,6, 7,8,9),{0,.1,.25)11,TableHeadings->{{111 = 0 M " , " I = 0.10 M",lnI = 0.25 M1'),{"pH 5","pH 7","pH 81t,11pH 911))1 6ii,m1pH PH 5

PH 6

PH 7

PH 8

I = O M

13815.3

18871.6

67452.

413294.

6 1.15554 10

I = 0.10 M

23226.8

36763.7

163714.

932920.

6 2.1999 10

I = 0.25 M

27548.

46145.7

218750.

6 1.20217 10

6 2.73926 10

PH 9

TableForm[(1/(8.3145l*.298l5*Log[lOl))*D[(co2tot+acetylcoA+nadred-pyruvate-coA-nadoxh2o),pH]/.is->{0,.1,.25)/.pH->(5,6,7,8,9},T~leHeadings->{{"I = 0 M","I = 0.10 M","I = 0.25 M"),{"pH 5 1 1 , " p H 6","pH 7","pH 8","pH 9")11

Thermodynamics of Biochemical Reactions at Specified pH

I = O M

PH 5 -0.0408172

PH 6 -0.296603

PH 7 -0.771728

PH 8 -0.687435

PH 9 -0.235697

I = 0.10 M

-0.0651484

-0.406673

-0.812946

-0.592257

-0.237883

I = 0.25 M

-0.0755408

-0.444665

-0.81951

-0.559928

-0.257158

309

Citrate synthase TableForm[Transpose[calctrGerx[acetylcoA+oxaloacetate+h2o+de==c~trate+coA,~5,6,7,8,9~,~ 0,.1,.25}11,TableHeadings->{{"I = 0 M","I = 0.10 M","I = 0.25 M"},{"pH 5","pH 6","pH 711,11pH 811,11pH 9v1}}] I = O M

PH 5 -37.3535

PH 6 -37.1217

PH 7 -40.2877

PH 8 -46.2697

PH 9 -55.1332

I = 0.10 M

-36.9892

-38.7412

-43.6084

-50.3226

-59.8309

I = 0.25 M

-37.0791

-39.5563

-44.7706

-51.6711

-61.3642

TableForm[Transpose[calck~rime[acetylcoA+oxaloacetate+h2o+de==c~trate+coA,{5,6,7,8,9~,~ 0,.1,.25)]],TableHeading~->{{'~I = 0 M","I = 0.10 M","I = 0.25 M"),{"pH 5","pH 6","pH 7","pH 811,"pH 9'*)}] PH 5

PH 6

PH 7

PH 8

PH 9

I = O M

6 3.49956 10

I = 0.10 M

6 3.02131 10

6 6.12526 10

7 4.36333 10

8 6.54759 10

10 3.03295 10

I = 0.25 M

6 3.13288 10

6 8.51005 10

7 6.97298 10

9 1.12808 10

10 5.62969 10

7 1.14305 10

6 3.18713 10

8 1.27658 10

9 4.55901 10

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(citrate+coA-acetylcoA-oxaloacetateh2o),pH]/.is->{O, .l, .25}/.pH->{5,6,7,8,9},TableHeadings->{{1nI = 0 M","I = 0.10 M","I = 0.25 Msw),{lmpH511,iipH 6","pH 7","pH 8 " , 1 1 p H 9ie)11 PH 5

0.32869

PH 6 -0.242031

PH 7 -0.839947

PH 8 -1.27037

PH 9 -1.80428

I = 0.10 M

0.0241225

-0.634751

-1.01063

-1.40059

-1.87189

I = 0.25 M

-0.0928804

-0.742845

-1.04053

-1.44166

-1.88881

I = O M

Aconitase TableForm[Transpose[calctrGerx[c~trate+de==acon~~atec~s+h2o,(5,6,7,8,9~,~O,.~,.25~ll,Ta bleHeadings->{{"I = 0 M","I = 0.10 M","I = 0.25 M"},{"pH 5","pH 6","pH 7"."pH 8","pH 9"))l I = O M

PH 5 17.5023

PH 6 11.5531

PH 7 8.92005

PH 8 8.43053

PH 9 8.37612

I = 0.10 M

13.4649

9.49365

8.50571

8.38388

8.37139

I = 0.25 M

12.3689

9.12025

8.45494

8.37861

8.37086

TableForm[Transpose[calckpr~e[citrate+de==acon~tatec~s+h2or{5,6,7,8,9~,~0,.1..2511l,Ta bleHeadings->{{@'I = 0 M","I = 0.10 M","I = 0.25 M i i } , { i i p H 51',"pH 6"."pH 7"."pH 8"."pH 9"))l

310

Mathernatica Solutions to Problems

I = O M

PH 5 0.000858528

PH 6 0.00946228

PH 7 0.0273705

PH 8 0.033346

PH 9 0.034086

I = 0.10 M

0.00437581

0.0217167

0.0323499

0.0339794

0.034151

I = 0.25 M

0.0068089

0.025247

0.0330192

0.0340517

0.0341583

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(aconitatec~s+h2o-c~trate),gHl/.~s>{0,.1,.25}/.pH->{5,6,7,%,9},TableHeadings->{{'1I = 0 M1l,"I = 0.10 M","I = 0.25 M"},{iipH 5'*,''pH 6 t v , 1 1 g H 7 ' m , 1 1 g H 8 " , 1 1 p H 9 m 1 } } 1

I = O M

PH 5 -1.32911

PH 6 -0.762126

PH 7 -0.200124

PH 8 -0.0241339

PH 9 -0.00246441

I = 0.10 M

-1.02481

-0.372043

-0.0533865

-0.0055862

-0.000561228

I = 0.25 M

-0.907921

-0.265114

-0.0337371

-0.00346956

-0.000347946

Aconitase TableForm[Transgose[calctrGerx[aconitatecis+h2o+de==c~trateiso,{5,6,7,8,9~,{O,.l,.25~ll ,TableHeadings->{{liI = 0 M","I = 0.10 M","I = 0.25 M"},{mlgH 5","gH 6","pH 7 m 1 , " p H 8","gH 9 1 1 } } 1 I = O M

PH 5 -10.8055

PH 6 -4.92275

PH 7 -2.27779

PH 8 -1.7815

PH 9 -1.72622

I = 0.10 M

-6.81316

-2.85648

-1.85783

-1.73411

-1.72141

I = 0.25 M

-5.72527

-2.4798

-1.80629

-1.72875

-1.72088

TableForm[:Trans~ose[calckprime[acon~tatec~s+h2o+de==c~trate~so,~5,6,7,8,9~,~O,.1,.25}11 ,TableHeadings->{{"I = 0 M","I = 0.10 M","I = 0.25 M"},{"gH 5","pH 6","gH 7","gH 8","gH 9 " ) ) J I = O M

PH 5 78.1691

PH 6 7.28489

PH 7 2.5064

PH 8 2.05165

PH 9 2.0064

I = 0.10 M

15.6173

3.16542

2.11581

2.0128

2.00252

I = 0.25 M

10.0697

2.71919

2.07227

2.00846

2.00209

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[~citrateiso-aconitatecis-h2o~,~H~ /.is>C0,.1,.25}/.pH->{5,6,7,8,9),TableHeadings->{{11I = 0 Mnl,"I= 0.10 M","I = 0.25 M" 1, C "pH 5", "pH 6", "pH 7 " , " p H 8", l'pH 9 " ) 1 I

I = O M

PH 5 1.30605

PH 6 0.760857

PH 7 0.202526

PH 8 0.0245142

PH 9 0.00250437

I = 0.10 M

1.0124

0.374671

0.0541865

0.00567633

0.00057035

I = 0.25 M

0.899474

0.267618

0.0342572

0.00352569

0.000353603

Isocitrate dehydrogenase TableFo~[Transpose[calctrGerx[:citrateiso+nadox+h2o+de==ketoglutarate+co2tot+nadred,~5, 6,7,8,9},{0,.1,.25}]],Tab1eHeadings->{{'11 = 0 M","I = 0.10 M","I = 0.25 M"},{"gH 5","pH 6 * * , " g H 7 * * , " p H 8 " , 1 1 p H 9 v 1 ) > 1

I = O M

PH 5 8.34114

PH 6 1.67592

PH 7 -4.21769

PH 8 -9.97115

PH 9 -15.7852

I = 0.10 M

5.50847

0.398237

-4.45015

-10.0157

-15.9678

I = 0.25 M

4.78775

0.245626

-4.45696

-10.0274

-16.0697

Thermodynamics of Biochemical Reactions at Specified pH

311

TableForm[Transpose[calckgrime[citrateiso+nadox+h2o+de==ketoglutarate+co2tot+nadred,~5, = 0 M*m,lmI = 0.10 M","I = 0.25 M"},{"pH 6,7,8,9),{0,.1,.25)]],Tab1eHeadings->{{111 5 ' 1 , 1 ' p H 6",11pH 7","pH 8"."pH 91m))]

I = O M

PH 5 0.0345704

PH 6 0.50862

PH 7 5.48156

PH 8 55.8289

PH 9 582.674

I = 0.10 M

0.108383

0.851594

6.02043

56.8417

627.221

I = 0.25 M

0.144953

0.905667

6.03701

57.1107

653.532

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(ketoglutarate+co2tot+nadred-c~trate~so-nadoxh20) ,pH] / .is-> (0, 1, .25 ) / .pH->{ 5,6,7,8,9) ,TableHeadings->{ {"I = 0 M", "I = 0.10 M " ,"I = 0.25 Msl),{iipH5","pH 6","pH 7","pH 8","pH 9"))l

.

I = O M

PH 5 -1.34729

PH 6 -1.06162

PH 7 -1.01433

PH 8 -1.00645

PH 9 -1.04494

I = 0.10 M

-1.07823

-0.788138

-0.931153

-1.00411

-1.1109

I = 0.25 M

-0.975816

-0.720242

-0.928031

-1.00858

-1.14667

ketoglutarate dehydrogenase Tab~eForm~Transpose~calctrGerx[ketoglutarate+nadox+coA+h2o+de==succinylcoA+co2tot+nadre d,~5,6,7,8,9},~0,.1,.25)11,TableHeadings-~{{~m1 = 0 M1l,*lI = 0.10 M","I = 0 . 2 5 M"},{"pH 5","pH 6","pH 7","pH 8","pH 9"))]

I = O M

PH 5 -32.2272

PH 6 -32.6665

PH 7 -35.7881

PH 8 -40.2782

PH 9 -42.8267

I = 0.10 M

-32.1519

-33.08

-36.7606

-41.0722

-43.1986

I = 0.25 M

-32.1464

-33.2446

-37.0834

-41.3056

-43.347

TableForm[Transpose[calckprime[ketoglutarate+nadox+coA+h2o+de==succinylcoA+co2tot+nadre d,{5,6,7,8,9),{0,.1,.25)11,TableHeadings->{{1~1 = 0 Mrm,"I = 0.10 M","I = 0.25 M"I,{"pH 5","pH 6","pH 7","pH 8","pH 9"))]

PH 5

PH 6

PH 7

PH 8

PH 9

528319.

6 1.86112 10

I = O M

442519.

I = 0.10 M

429279.

624208.

6 2.75508 10

7 1.56857 10

7 3.69848 10

I = 0.25 M

428331.

667072.

6 3.1383 10

7 1.72338 10

7 3.92659 10

7 1.13869 10

7 3.18322 10

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(succinylcoA+co2tot+nadred-ketoglutaratenadox-coA-h2o),pHI/.is->{O,.l,.25}/.pH->{~,6,7,8,9},TableHeadings->{{"I = 0 M","I = 0.10 M 1 l , l i I = 0.25 M1l),{llpH5m1,11pH 611,"pH 7","pH 8","pH 9"))l

I = O M

PH 5 0.0991751

PH 6 -0.280585

PH 7 -0.770103

PH 8 -0.687272

PH 9 -0.235683

I = 0.10 M

0.0252188

-0.396837

-0.811953

-0.592158

-0.237873

I = 0.25 M

0.00254914

-0.436266

-0.818663

-0.559843

-0.25715

Succinyl coA synthase

312

Mathematica Solutions

to

Problems

I = O M

PH 5 11.3123

PH 6 9.42916

PH 7 6.0856

PH 8 4.60067

PH 9 1.48513

I = 0.10 M

8.64828

5.44782

2.53412

0.710067

-3.18751

I = 0.25 M

7.58697

4.09308

1.26214

-0.651704

-4.72216

TableForm[Transpose[calckgrime[succinylcoA+gi+adg+de==succinate+atg+coA,{5,6,7,8,9~,{0, .1,.25)]],TableHeadings->{{~'I = 0 M","I = 0.10 M","I = 0.25 M"),{"pH 5","gH 6","gH 7","gH 8","gH 9")}]

I = O M

PH 5 0.0104276

PH 6 0.0222891

PH 7 0.0858727

PH 8

0.156315

PH 9 0.549312

I

0.10 M

0.0305419

0.111068

0.359786

0.750935

3.61763

I = 0.25 M

0.0468627

0.191835

0.601012

1.30069

6.71864

=

TableForm[(1/(8.3145l*.298l5*Log[lOl))*D[(succinate+atg+coA-succ~nylcoA-p~adg),gH]/.is->{O, .l, .25}/.pH->{5,6,7,8,9},TableHeadings->{{*'I = 0 M " , " I = 0.10 M","I = 0.25 M1m},{tlpH 511,11pH 611,11gH 711,1tpH 8","gH 911))1

I = O M

PH 5 -0.0431903

PH 6 -0.591126

PH 7 -0.421843

PH 8 -0.27808

PH 9 -0.799126

I = 0.10 M

-0.347965

-0.659794

-0.328911

-0.443368

-0.876329

I

-0.436744

-0.660859

-0.321521

-0.47926

-0.892712

0.25 M

Succinate dehydrogenase TableForm[Trans~ose[calctrGerx[succinate+fadenzox+de==fumarate+fadenzred,~5,6,7,8,9~,~O ,.1,.25}]],TableHeadings->{{"I = 0 M",811= 0.10 M","I = 0.25 M 1 r ) , { " g H 5","pH 6","pH 7","pH 8","gH 9"}}1

I = O M

PH 5 3.58609

PH 6 0.778578

PH 7 0.0656228

PH 8 -0.0202505

PH 9 -0.0290231

I = 0.10 M

2.15463

0.30828

0.00611379

-0.0263635

-0.0296361

I = 0.25 M

1.7504

0.220992

-0.00368738

-0.0273557

-0.0297354

TableForm[Transgose[calckprime[succinate+fadenzox+de==fumarate+fadenzred,{5,6,7,8,9~,~O ,.1,.25)]],TableHeadings->{(8tI = 0 M1m,lmI = 0.10 M","I = 0.25 M"},{"pH 5","gH 6","pH 71*,11gH 811,11pH 9")}]

I = O M

PH 5 0.235369

PH 6 0.730466

PH 7 0.973876

PH 8 1.0082

PH 9 1.01178

I = 0.10 M

0.419303

0.883064

0.997537

1.01069

1.01203

I = 0.25 M

0.493565

0.914711

1.00149

1.0111

1.01207

TableForm[(1/(8.31451*.29815*Log[1O]))*D[(fumarate+fadenzred-succ~natefadenzox),pH]/.is->{O,.l,.25}/.gH->{5,6,7,8,9},TableHeadings->{{~~I = 0 M","I = 0.10 M","I = 0.25 M"},{"gH 5","pH 6","pH 7","pH 8","pH 9"))l

I = O M

PH 5 -0.658653

PH 6 -0.272415

PH 7 -0.0377549

PH 8 -0.00392427

PH 9

I = 0.10 M

-0.565671

-0.127042

-0.0144565

-0.0014658

-0.000146785

I = 0.25 M

-0.504786

-0.0961348

-0.0105565

-0.00106609

-0.000106714

Fumarase

-0.000393977

Thermodynamics of' Biochemical Reactions at Specified pH

313

TableForm[Transpose[calctrGerx[fumarate+h2o+de==~~ate,{5,6,7,8,9~,{O,.l,.25~ll,TableHe adings->{{'I = 0 M","I = 0.10 M","I = 0.25 Mii),{mmpH 5","pH 611,"pH7","pH 8","pH 9"I)l I = O M

PH 5 -5.32376

PH 6 -3.91639

PH 7 -3.63473

PH 8 -3.60351

PH 9 -3.60035

I = 0.10 M

-4.53418

-3.72559

-3.61302

-3.60131

-3.60013

0.25 M

-4.33506

-3.69229

-3.60948

-3.60095

-3.6001

I

=

TableForm[Transpose[calckpr~e~fumarate+h2o+de==ma~ate,{5,6,7,8,9~,~0,.~,.25~l1,TableHe adings->{{"I = 0 M","I = 0.10 M","I = 0.25 M1m),{tlpH5","pH 6","pH 7","pH 8","pH 9"))l

I = O M

PH 5 8.56401

PH 6 4.85419

PH 7 4.33284

PH 8 4.27862

PH 9 4.27317

I = 0.10 M

6.22801

4.4946

4.29507

4.27482

4.27279

I = 0.25 M

5.14132

4.43464

4.28894

4.27421

4.27273

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(~late-f~arate-h2o),pHl/.~s->~O,.l,.25~/.pH>{5,6,7,8,9),TableHeadi11gs->{{~~I= 0 M"."I = 0.10 M","I = 0.25 M"), {"pH 5","pH 6","pH 71m,11pH 811,11pH 9n1))]

I = O M

PH 5 0.353078

PH 6 0.115155

PH 7 0.0138543

PH 8 0.0014132

PH 9 0.000141603

I = 0.10 M

0.271995

0.0486631

0.00523192

0.000527102

0.0000527496

I = 0.25 M

0.230733

0.0361476

0.00381207

0.00038328

0.0000383488

[alate dehydrogenase TableForm[Transpose[calctrGerx[malate+nadox+de==oxaloacetate+nadred,{5,6,7,8,9~,~O,.l,. 2511 I ,TableHeadings->{{alI= 0 Mn,"I = 0.10 M',"I = 0.25 M"),{"pH 5"."pH 6","pH 7","pH 8","pH 9"))l I = O M

PH 5 46.0468

PH 6 38.1855

PH 7 32.1083

PH 8 26.3602

PH 9 20.6481

I = 0.10 M

42.3126

35.4858

29.6322

23.9091

18.1995

I = 0.25 M

41.2328

34.6521

28.8372

23.1182

17.4091

TableForm[Transpose[calck~rime[~alate+nadox+de==oxaloacetate+nadred,{5,6,7,8,9~,~O,.l,. 25}]] ,TableHeadings->{{"I = 0 M","I = 0.10 M","I = 0 . 2 5 M"), {"pH 5","pH 6","pH 7","pH 8rm,*3#I 9"))l I = O M

8.57032 10

2.04279 10

2.3708 10

0.0000240949

0.000241343

I = 0.10 M

-8 3.86543 10

-7 6.07008 10

-6 6.43723 10

0.000064764

0.000648034

I = 0.25 M

-8 5.97546 10

-7 8.49672 10

-6 8.87102 10

0.0000891027

0.000891421

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(oxaloacetate+nadred-~late-nadox),pHl/.~s>{0,.1,.25}/.pH->{5,6,7,8,9},TableHeadings->{{iiI = 0 M","I = 0.10 M","I = 0.25 M1l),{llpH5m1,"pH 6",'pH 7","pH 8","pH 9"))J

314

Mathernatica Solutions to Problems

I = O M

PH 5 -1.64496

PH 6 -1.15373

PH 7 -1.01784

PH 8 -1.00181

PH 9 -1.00018

I = 0.10 M

-1.40356

-1.06337

-1.00672

-1.00068

-1.00007

I = 0.25 M

-1.3297

-1.04688

-1.00489

-1.00049

-1.00005

Net reaction for the citric acid cycle TableForm[Transpose[calctrGerx[acetylcoA+3*nadox+fadenzox+adp+pi+4*h2o+de==2*co2tot+3*n adred+fadenzred+atp+coA, {5,6,7,8,9), {O, .l, .25)1 I .TableHeadings->{{"I = 0 M"."I = 0.10 M","I = 0.25 M1'I,{"pH 5'1,"pH 6",1mpH7","pH 8","pH 9"))l I = O M

PH 5 1.07855

PH 6 -17.0051

PH 7 -39.0265

PH 8 -62.5329

PH 9 -88.5914

I = 0.10 M

-8.39957

-27.2695

-49.6119

-73.7693

-100.965

I

-11.5591

-30.641

-53.1761

-77.5161

-105.074

=

0.25 M

TableForm[Transpose[calck~rime[acetylcoA+3*nadox+fadenzox+ad~+p~+4*h2o+de==2*co2tot+3*n adred+fadenzred+atp+coA,{5,6,7,8,9},{O,.l,.25~~l,Table~eadings-~{~"I = 0 M","I = 0.10 M","I = 0.25 M"),{"pH 5","pH 6","pH 7","pH 8","pH 9"))l

PH 5

PH 6

PH 7

PH 8

PH 9

953.103

6 6.87231 10

I = O M

0.647214

I = 0.10 M

29.6165

59893.3

8 4.91554 10

12 8.38962 10

11 4.87771 10

I = 0.25 M

105.938

233370.

9 2.07014 10

13 3.80323 10

18 2.55874 10

10 9.02059 10

15 3.31471 10

TableForm[(1/(8.3145l*.298l5*Log[lOl))*D[(2*co2tot+3*nadred+fadenzred+at~+coAacetylcoA-3*nadox-fadenzox-ad~-pi-4*h2o),pHl/.is-~{O,.l,.~~}/.~H>{5,6,7,8,9},TableHeadings->{{"I = 0 M1l,nlI = 0.10 M"."I = 0.25 M*tl,{llpH 5","pH 6","pH 711,vigH 8 1 1 , " g H 911))]

I = O M

PH 5 -2.9362

PH 6 -3.48762

PH 7 -4.08556

PH 8 -4.24612

PH 9 -4.88442

I

-3.08649

-3.61864

-4.0978

-4.44174

-5.09714

-3.1151

-3.66458

-4.11986

-4.49046

-5.18546

=

0.10 M

I = 0.25 M

Net reaction for the pyruvate dehydrogenase reaction plus the citric acid cycle (10 reactions) TableForm[Transgose[calctrGerx[pyruvate+4*nadox+fadenzox+adp+pi+5*h2o+de==3*co2tot+4*na dred+fadenzred+atp, {5,6,7,8,9), { O , .l, .25)]] ,TableHeadings->{{"I = 0 M","I = 0.10 M","I = 0.25 M"),{"pH 5","pH 6","pH 7","pH 8","pH 9 " > ? 1

I = O M

PH 5 -22.5548

PH 6 -41.4116

PH 7 -66.5906

PH 8 -94.5908

PH 9 -123.198

I

0.10 M

-33.3208

-53.3291

-79.3741

-107.845

-137.168

I = 0.25 M

-36.9033

-57.2641

-83.6568

-112.221

-141.82

=

TableForm[Trans~ose[calck~rime[pyruvate+4*nadox+fadenzox+ad~+p~+5*h2o+de==3*co2tot+4*na dred+fadenzred+atp, {5,6,7,8,9), {O, .l, -2511],TableHeadings->{ {"I 0 M", "1 = 0.10 M", "I = 0.25 M"),{"pH 5","pH B","pH 7","pH 8","pH 9"))l 5

Thermodynamics of Biochemical Reactions at Specified pH PH 5

PH 6

PH 7

PH 8

PH 9

4.63551 10

16 3.72816 10

21 3.83029 10

I = O M

8941.45

7 1.79866 10

I = 0.10 M

687894.

9 2.2019 10

13 8.04744 10

18 7.82684 10

24 1.07305 10

I = 0.25 M

6 2.91838 10

10 1.0769 10

14 4.52844 10

19 4.57215 10

24 7.00906 10

11

315

TableForm[~1/(8.3145l*.298l5*Log[lO]))*D[(3*co2tot+4*nadred+fadenzred+atgpyruvate-4*nadox-fadenzox-ad~-pi-5*h2o),pH]/.is-~{O,.l,.2S}/.~H>{5,6,7,8,9),TableHeadings->{{1rI = 0 M",glI = 0 . 1 0 M"."I = 0.25 M1l),{l'gHS","gH 6","gH 7","pH 8","pH 9"))l

I = O M

PH 5 -2.97701

PH 6 -3.78422

PH 7 -4.85728

PH 8 -4.93355

PH 9 -5.12012

I = 0.10 M

-3.15164

-4.02532

-4.91074

-5.034

-5.33503

I = 0.25 M

-3.19064

-4.10924

-4.93937

-5.05039

-5.44262

Net reaction for glycolysis, pyruvate dehydrogenase, and the citric acid cycle TableForm[Transpose[calctrGerx[glucose+lO*nadox+2*fadenzox+4*a~p+4*p~+8*h2o+de==6*co2to t+l0*nadred+2*fadenzred+4*at~,{5,6,7,8,9},{O,.l,.25}ll,TableHead~ngs-~{{1~I= 0 M","I = 0 . 1 0 M"."I = 0.25 Mrm},{llpH 511,*1pH 6 1 1 , " p H 7","pH 8","pH 9"))l I = O M

PH 5 -72.0125

PH 6 -131.329

PH 7 -201.137

PH 8 -270.179

PH 9 -338.639

I = 0.10 M

-104.897

-166.593

-236.258

-306.076

-376.313

I = 0.25 M

-115.897

-178.144

-248.124

-318.007

-388.781

TableForm[Transpose[calck~rime[glucose+lO*nadox+2*fadenzox+4*adg+4*p~+8*h2o+de==6*co2to = 0 M","I = t+l0*nadred+2*fadenzred+4*at~,~5,6,7,8,9~,~O,.l,.2S~ll,TableHeadin~s-~~~"~ 0.10 M","I = 0.25 M"),{"pH 511,m1pH 61s,"pH 7","pH 8","pH 9">)1

I = 0.10 M

PH 5 12 4.13017 10 18 2.38257 10

I = 0.25 M

2.01437 102o

I = O M

PH 6 1.01782 1023 29 1.53315 10 31 1.61917 10

PH 7 35 1.72759 10 41 2.45688 10 43 2.94593 10

PH 8 47 2.15268 10 53 4.18709 10 55 5.15271 10

PH 9 59 2.12147 10 65 8.4501 10 68 1.29175 10

TableForm[(1/(8.3145l*.298l5*Log[lO]))*D[(6*co2tot+lO*nadred+2*fadenzred+4*atgglucose-l0*nadox-2*fadenzox-4*ad~-4*~i-8*h2o),pH]/.is->{O,.l,.25~/.~H>(5,6,7,8,9},TableHeading~->{{~I = 0 M","I = 0 . 1 0 M","I = 0.25 M"), {"gH 5","pH 6"."gH 7","pH 8 " , I 1 p H 9")}1

PH 5 -9.66065

PH 6 -11.3323

PH 7 -12.5583

PH 8 -11.8426

PH 9 -12.2258

0.10 M

-10.2116

-11.6205

-12.3812

-12.1454

-12.6781

I = 0.25 M

-10.3045

-11.7212

-12.3948

-12.1712

-12.8926

I = O M I

=

Chapter 5 Matrices in Chemical and Biochemical Thermodynamics 5.1 (a) Carry out the operations involved in equations 5.1-12 to 5.1-27 using MathematicaR. (b) Carry out the operations involved in equations 5.1-22 to 5.1-26. (c) Calculate the amounts of the components C, H, and 0 for a system containing one mole of each of the five species. (d) Calculate the amounts of the components CO, H I , and CH4 for the system containing one mole of each of the five species.

5.2 (a) Construct the conservation matrix for the hydrolysis of ATP to ADP in terms of species. (b) Calculate a basis for the stoichiometric matrix from the conservation matrix and show that it is consistent with equations 5.1-28 to 5.1-31.

5.3 (a) Construct the conservation matrix A' for the hydrolysis of ATP to ADP in terms of reactants. (b) CafcuIate a basis for the stoichiometric matrix from the Conservation matrix and show that it is consistent with ATP + H2 0 = ADP + P,. 5.4 The glutamate-ammonia ligase reaction is glutamate + ATP + ammonia = glutamine + ADP + pi It can be considered to be the sum of two reactions. (a) Write the stoichiometric number matrix for this enzyme-catalyzed reaction and use NullSpace to obtain a basis for the conservation matrix.. (b) Write a conservation matrix that includes a constraint to couple the two subreactions, and row reduce it to show that it is equivalent to the stoichiometric number matrix obtained in (a).

5.5 Carry out the matrix multiplications in equation 5.4-4 for the three chemical reactions involved in the hydration of fumarate to malate in the pH range 5 to 9.

317

318

Matheniatica Solutions to Problems

5.1 (a) Carry out the operations involved in equations 5.1-12 to 5.1-27 using MathematicaR. (b) Carry out the operations involved in equations 5.1-22 to 5.1-26. (c) Calculate the amounts of the components C, H, and 0 for a system containing one mole of each of the five species. (d) Calculate the amounts of the components CO, H 2 , and CH4 for the system containing one mole of each of the five species.

(a) Equations 5.1-12 to 5.1-20 The conservation matrix is given by

TableForm [a] 1 0 1

0 2 0

1 4 0

0 2 1

1 0 2

The stoichiometric number matrix is given by

TableForm[nul -1 -3

1 1 0

-1 1 0 -1 1

The matrix product is given by TableForm[a.nul 0

0

0

0

0

0

The canonical form of the conservation matrix is TableForm[ared=RowReduce[all 1 0 0

0 1 0

0 0 1

1 3 -1

2 2 -1

The matrix product using the row reduced form of the conservation matrix isactivated by using a period. TableForm [ared.nu1 0 0 0

0 0 0

Thus the row reduced form represents the conservation relations equally well. Calculate a basis for the nullspace of the conservation matrices a.

Matrices in Chemical and Biochemical Thermodynamics

319

TableForm[Transpose[NullSpace[a]1 1 -2

-1

-2

-3

1 0

1 1

These are the same two reactions as in equation 5.1-20. (b) Equations 5.1-22 to 5.1-26. Now we start with the transpose of the stoichiometric number matrix. nutr=Transpose[nul

{{-I, - 3 , 1, 1, O } , I - 1 ,

0

0

0

0

0

0

1, 0 , -1, 1 1 1

Now calculate a basis for the transpose of the conservation matrix from the transposed stoichiometric number matrix. TableForm[NullSgace[nutrlI

- 1 1 1 1

3

1

0

0

4

0

2

0

4

0

0

This looks different from equation 5.1-8, but yields 5.1-15 when RowReduction is used. TableFonn[RowReduce~NullSpace[nutrll1

1 0 0

0 1 0

0 0 1

1 3 -1

2

2

-1

The rank of the conservation matrix is the number of components, which is 3. Dimensions [a] ( 3 , 5)

The rank of the stoichiometric number matrix is equal to the number of independent reactions, which is 2. Dimensions [nu] (5,

2)

(c) Calculate the amounts of the components C, H, and 0 for a system containing one mole of each of the five species. Equation 5.1-27 yields a. {l,l,l, 1,l)

320

Mathematica Solutions to Problems

{ 3 , 8,

41

Note that Mathernatica makes no distinction between "row" and "column" vectors. (d) Calculate the amounts of the components CO, H,, and CH4 for the system containing one mole of each of the five species. ared.{l,l,l,l,l}

Note that the amount of a component can be negative. 5.2 (a) Construct the conservation matrix for the hydrolysis of ATP to ADP in terms of species. (b) Calculate a basis for the stoichiometric matrix from the conservation matrix and show that it is consistent with equations 5.1-28 to 5.1-31. (a) Construct the conservation matrix for the hydrolysis of ATP to ADP in terms of species. a={{10,0,0,0,10,10,10,0}, ;

{12,1,2,1,12,13,13,2},

{13,0,1,4,10,13,10,4},

{3,0,0,1,2,3,2,111

TableForm[a,TableHeadings-> { { " C " ,"H"," 0 ","P"} ,{ "ATPI-", "H+","H20", "HP042-"," m P 3 iiHATP3I # ,W A D P 2 "H2P04- 1 1, Tablespacing-> E 1,1.5 1 I I*,

c

ATP410

H+ 0

H20 0

HP042- ADP30 10

HATP3- HADP210 10

H2P040

H

12

1

2

1

12

13

13

2

0

13

0

1

4

10

13

10

4

P

3

0

0

1

2

3

2

1

TableForm[RowFleduce[a],TableHeadings->{{ "ATP4-", "H+",1'H20",1'HP042-"},("ATP4' I , 'H+", "H20", 11HP042-11, "ADP3-1 1 , "HATP3-'I, "KADPS-' I , "H2PO4- } 1, Tablespacing-> { 1,l. 5 11

ATP4-

ATP41

H+ 0

H20 0

HP042- ADP30 1

HATP3- HADP21 1

H2P040

H+

0

1

0

0

-1

1

0

1

H20

0

0

1

0

1

0

1

0

HP042-

0

0

0

1

-1

0

-1

1

(b) Calculate a basis for the stoichiometric matrix from the conservation matrix and show that it is consistent with equations 5.1-28 to 5.1-31. TableForm[nu=~llSpace [a]1

0 - 1 0 - 1 0 - 1 - 1 - 1 0 - 1 1 - 1

1 0 1

1

0 0 1

0

0 1 0

0

0 1 0 0

1 0 0 0

The transposed stoichiometric matrix for reactions 5.1-28 to 5.1-31 is nutrexpected={E-l,l,-l,l,l,O,O,O},{l,l,O,O,O,-l,O,O},{O,l,O,O,l,O,-l,O},~O,l,O,l,O,O,O, -111;

Matrices in Chemical and Biochemical Thermodynamics

321

TableFonu [nutrexpected,TableHeadings-> { { * l r x l l n"rx2 , ' I , 11rx311, *1rx4" 1, { "ATP4'I, "H+","H20", "HP042-", "ADP3-", "HATP3-" ,"HADP2-" ,"H2P04-"1 } 1 ATP4-

-1

H+

H20 -1

HP042-

ADP3-

HATP3-

HADP2-

H2P04-

rxl rx2

1

1

0

0

0

-1

0

0

rx3

0

1

0

0

1

0

-1

0

rx4

0

1

0

1

0

0

0

-1

1

1

1

0

0

0

We can check whether NullSpace[a] and nuexpected are equivalent by row reducing each of them. TableForm [RowReduce[NUllSgace[a]1 1

1 0 0 0

0 0 0 - 1 - 1 1 0 1 0 0 1 0 - 1 0 0 1 0 0 1 - 1 - 1 0 0 1 - 1 0 1 - 1

TableForm[RowReduce[nutrexpectedll 1 0 0 0

0 0 0 - 1 - 1 1 0 1 0 0 1 0 - 1 0 0 1 0 0 1 - 1 - 1 0 0 1 - 1 0 1 - 1

Since these last two matrices are identical, NullSpace[a] and nuexpected are equivalent.

5.3 (a) Construct the conservation matrix A' for the hydrolysis of ATP to ADP in terms of reactants. (b) Calculate a basis for the stoichiometric matrix from the conservation matrix and show that it is consistent with ATP + HI0 = ADP + Pi. (a) Construct the conservation matrix for the hydrolysis of ATP to ADP in terms of reactants.

TablePorm[aa,TableHeadings->{ { a s C m"rO, " , "P"), {"ATP", "H20", "ADP", ''Pi''} 11

c

ATP

H20

ADP

Pi

0

13

1

10

4

P

3

0

2

1

10

0

10

0

TableForm[RowReduce[aal ,TableHeadings->{ {llATP1l, 11H20m1, a'ADP1l), {''ATP", "H20", "ADP",''Pi"1 1 1 ATP

ATP 1

H20 0

ADP 0

Pi 1

H20

0

1

0

1

ADP

0

0

1

-1

(b) Calculate a basis for the stoichiometric number matrix from the conservation matrix. TableForm[nu=NullSgace[aa],TableHeadings->{{"rx"}, {"ATP", "H20". IIADPml, "Pi1'}11 ATP

rx

-1

H20

-1

ADP

1

Pi 1

322

Mathematica Solutions to Problems

This is the expected stoichiometric number matrix. 5.4 The glutamate-ammonia ligase reaction is

glutamate + ATP + ammonia = glutamine + ADP + Pi It can be considered to be the sum of two reactions. (a) Write the stoichiometric number matrix for this enzyme-catalyzed reaction and use Nullspace to obtain a basis for the conservation matrix.. (b) Write a conservation matrix that includes a constraint to couple the two subreactions, and row reduce it to show that it is equivalent to the stoichiometric number matrix obtained in (a). (a) Calculate a basis for the conservation matrix from the stoichiometric number matrix and row reduce it. TableForm[NullSgace[~~-l,-l,-l,l,1,l~~ll

1 1 1 -

0 0 0 1 1

0 0 0

0 1

1 0 0 0 0

0 1 0 0 0

0 0 0 1 0 0 0 1 1 0 0 1 0 1 0 - 1 0 0 1 - 1

1 0

0 0 1

0 1 0 0 0 0 0

1 0 0 0 0

This shows that there are five components, in spite of the fact that there are just four elements (C, 0, N, P). (b) Write the apparent conservation matrix for the glutamate-ammonia ligase reaction and row reduce it. One way to couple the two subreactions is to require that every time an ATP molecule disappears, a glutamine molecule appears; this leads to the conservation equation n(ATP) + n(g1utamine) = const

0

4

13

0

10

4

3

N

1

5

1

5

0

2

P

0

3

0

2

1

0

con1

0

1

0

0

0

1

TableForm[RowReduce [a],TableHeadings> { { "Glamatel*, "ATP",llAwn", "ADP", m l P i m l {} ,"Glutmatell, llATP1lr llAmmll, "ADP" ,"Pi",llGlutmine"} }]

Matrices in Chcrnical and Biochemical Thermodynamics Glutmate 1

ATP 0

Amm

ADP

0

Pi 0

Glutmine 1

ATP

0

1

0

0

0

1

Amm

0

0

1

0

0

1

ADP

0

0

0

1

0

-1

Pi

0

0

0

0

1

-1

Glamate

0

323

Since this yeids the same row reduced conservation matrix as (a), the stoichiometric number matrix and the conservation matrix are equivalent.

5.5 Carry out the matrix multiplications in equation 5.4-4 for the three chemical reactions involved in the hydration of fumarate to malate in the pH range 5 to 9. First we construct the stoichiometric number matrix (eqation 5.4-9) and the vector of chemical potentials. Matrix 5.4-9 is given by

F2-

rx5 -1

rx6 1

rx7 0

M2-

1

0

1

HF-

0

-1

0

HM-

0

0

-1

H+

0

1

1

H20

-1

0

0

mu= { {muF,muM,muHF,muHM,muH,muIi20} 1 ;

Next we calclate the dot product of the chemical potential vector and the stoichiometric number matrix. mu. nu

{{-muF - m u H 2 0 + muM, muF + m u H - m u H F , muH - muHM + muM}) The column matrix of extents of reaction is given by

TableForm [XI

xl x2 x3

The last term in equation 5.4-4 is given by mu. nu. x

{{(-muF

-

m u H 2 O + muM) xl

This corresponds with equation 5.4-10.

+ (muF + muH

- m u H F ) x2 + (muH - muHM

+

muM) x 3 } }

Chapter 6 Systems of Biochemical Reactions 6.1 Make the stoichiometric number matrix for reactions 6.5-17 to 6.5-19 and use it to print out these reactions. 6.2 Calculate the pathway from glucose to carbon dioxide and water in terms of (1) the net reaction for glycolysis, (2) the net reaction catalyzed by the pyruvate dehydrogenase complex, (3) the net reaction for the citric acid cycle, and (4) the net reaction for oxidative phosphorylation. 6.3 (a) Type in the stoichiometric number matrix for glycolysis at a specified pH that is given in Fig. 6.1. (b) Use nameMatrix to type out the 10 reactions. (c) Use equation 6.1-3 to calculate the net reaction for glycolysis. (d) Calculate a basis for the conservation matrix for glycolysis and row reduce it to determine the number of components. 6.4 The following reaction is carried out enzymatically at 298.15 K, pH 7, and 0.25 M ionic strength. ATP + glucose = glucose6phos + ADP The initial concentrations of ATP and glucose are 0.001 M. What is the equilibrium composition? Solve this problem using Mathernatica in two ways.

6.5 Calculate the apparent equilibrium constant for the net reaction for the first five reactions of glycolyis that is, reactions 6.6-1 to 6.6-5) using equation 6.1-6. Check this by simply using the net reaction.

'-,

and 0.01 mol Mg2+.Assuming that the ionic 6.6 A liter of aqueous solution contains 0.01 mol Hz PO4 - , 0.01 mol H P 0 4 strength is zero, what is the equilibrium composition of the solution in terms of species at 298.15 K? 6.7 When 0.01 M glucose 6-phosphate is hydrolyzed to glucose and phosphate at 298.15 K in the pH range 9-10, only four species have to be considered. G l c P 2 - + Hz 0 = Glc + H P 0 4 2 What is the equilibrium composition assuming the ionic strength is zero? 6.8 A liter of aqueous solution contains 0.02 mol phosphate and acid and NaCl are added to bring it to pH 7, and 0.25 M ionic strength. What is the equilibrium composition in terms of phosphate species?

325

326

Mathematica Solutions to Problems

6.1 Make the stoichiometric number matrix for reactions 6.5-17 to 6.5-19 and use it to print out these reactions.

TableForm t nu 1

-1 -1 1 1 0 0

0 0 -1 0 1 0

0 -1 0 1

-1 1

TableForm[nu,TableHeadings->{names3, {"rx 1311,1mrx 14". "rx 15")}]

rx 13

rx 14

rx 15

ATP

-1

0

-1

G6P

1

-1

0

ADP

1

0

1

F6P

0

1

-1

F16BP

0

0

1

Glc

-1

0

0

mkeqm[c-List,s-List]:=(*c-List is the list of stoichiometric numbers for a reaction. s-List is a list of the names of species or reactants. These names have to be put in quotation marks. * 1Map [MaxI#, 0I &, -cl s->Map [Max[ #, 0I &, cl s

.

.

nameMatrix[m-List,s-List]:=(*m-List is the transposed stoichiometric number matrix for the system of reactions. s-List is a list of the names of species or reactants. These names have to be put in quotation marks.*)Map[mkeqm[#,sl&,ml mkecp [ { -1, -1,l, 1,0,0 1, names31 ATP + G l C -> ADP + G6P

nameMatrix [Transpose[nu1,names3 1 {ATP

+

GlC -> ADP + G6P, G6P -> F 6 P , ATP + F6P - > ADP + F16BP)

6.2 Calculate the pathway from glucose to carbon dioxide and water in terms of (1) the net reaction for glycolysis, (2) the net reaction catalyzed by the pyruvate dehydrogenase complex, (3) the net reaction for the citric acid cycle, and (4) the net reaction for oxidative phosphorylation. The stoichiometric number matrix for these four reactions is

TableForm[nu4,TableHeadings->{names,Automatic}l

Systems of Biochemical Reactions 1

2

3

4

Glc

-1

0

0

0

Pi

-2

0

-1

-3

ADP

-2

0

-1

-3

NADox

-2

-1

-4

1

PYr

2

-1

0

0

ATP

2

0

1

3

NADred

2

1

4

-1

H20

2

0

-2

4

CoA

0

-1

1

0

acetylCoA

0

1

-1

0

c02

0

1

2

0

327

1

0

02

0

0

- (-)

2

mkeqm[c-List,s-List]:=(*c-List is the list of stoichiometric numbers for a reaction. s-List is a list of the names of species or reactants. These names have to be gut in quotation marks. * )Mag [Max[#, 01 &, -cl s->Mag[Max[#, 0 I &, cl s

.

.

nameMatrix[m~List,s~Listl:=(*m~List is the transposed stoichiometric number matrix for the system of reactions. s-List is a list of the names of species or reactants. These names have to be gut in quotation marks.*)Map[mkeqm[#,sl&,ml

nameMatrix[Transgose~nu~~ ,names1 {2 ADP + Glc + 2 NADox + 2 Pi -> 2 ATP + 2 H20 + 2 NADred + 2 Pyr, CoA + NADox + Pyr -> acetylCoA + C02 + NADred, acetylCoA + ADP + 2 H20 + 4 NADox + Pi -> ATP + 2 C02 + CoA + 4 NADred,

3 ADP + NADred + - + 3 Pi -> 3 ATP + 4 H20 + NADox} 2

As indicated in equation 6.2-2 the stoichiometric numbers for the net reaction are given by nunet={-1,-40,-40,0,0,46,0,0,6,0,0r6,-61

{-I, - 4 0 ,

-40, 0 , 0 , 4 0 , 0 , 4 6 , 0 , 0 , 6 , - 6 1

The pathway can be calculated by use of

Thus to oxidize a mole of glucose to carbon dioxide and water, reaction 1 has to occure once, reaction 2 has to occur twice, reaction 3 has to occur twice, and reaction 4 has to occur 12 times.

6.3 (a) Type in the stoichiometric number matrix for glycolysis at a specified pH that is given in Fig. 6.1. (b) Use nameMatrix to type out the 10 reactions. (c) Use equation 6.1-3 to calculate the net reaction for glycolysis. (d) Calculate a basis for the conservation matrix for glycolysis and row reduce it to determine the number of components.

328

Mathematica Solutions to Problems

(a) The stoichlometric number matrix for glycolysis

TableForm[nu2,TableHeadings->{n~es2,{1,2,3,4,5,6,7,8,9,lO}}l

4

5 0

6

0

0

0

1

0

0

0

N A D r e d O

0

Pi

0

0

G6P

1

F6P

0

1

FBP

0

0

1

DHAP

0

0

0

1

13BPG

0

0

0

0

3PG

0

0

0

2PG

0

0

PEP

0

GAP PY r

7 0

8

9

10 0

0

1

0

0

1

0

0

-1

0

0

-1

0

0

-

0

0

0

O

0

0

0

1

0

0

0

0

0

0

0

-

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

0

1

-1

0

O

0

0

0

0

1

0

0

0

0

0

0

0

1

0

0

0

0

0

0

0

1

0

0

0

1

1

-

0

0

0

0

0

0

0

0

0

0

0

0

1

G 1c

1 -

1

2 0

3 0

ATP

-

1

0

-

ADP

1

0

NADOX

0

-

1 -

1

1 -

1 -

0

1

1

1

1

0

-

0

0

1 -

1

0

-

1

This is Fig. 6.1. (b) Use mathematica to type out the reactins of glycolysis

.

.

mkeqm [c-List ,s-List ]:=Map [Max[ #, 01 &, -cl s->Mag[MaxI#, 01 &, Cl S nameMatrix [m-Li St ,s-Lis t 1 :=Map [mkeqm[ # ,s 1 & ,ml

{ATP + G l C -> ADP DHAP -> GAP, GAP 3PG -> 2 P G ,

+

G 6 P , G 6 P -> F 6 P , ATP + F 6 P - > ADP + F B P , F B P - > DHAP + GAP,

+ NADox +

P i -> 13BPG

+

N A D r e d , 1 3 B P G + ADP - > 3PG + A T P ,

2PG -> P E P , ADP + P E P -> ATP + P y r }

(c) Equation 6.1-3 (v.s = nunet) is given by nu2.{1,1,1,1,1,2,2,2,2,2}

Systems of Biochemical Reactions

329

{-1, 2, -2, -2, 2, -2, 0 , 0 , 0 , 0 , 0 , 0, 0 , 0 , 0 , 2 1 mke~[nu2.{1,1,1,1,lr2,2,2,2,2,2},n~es21 2 ADP + G l c + 2 NADox + 2 P i -> 2 A T P + 2 N A D r e d + 2 Pyr

(d) Use Mathematica to make Fig. 6.2. TableForm[Transpose[RowReduce[~llSpacetTrans~ose[nu2l11l,TableHeadings>{names2, { i i G l c n , i l A T P i i , iiADPii,iiNADoxll,iINADredLII, l l P i i l l11

Glc

Glc

1

0

ADP 0

NADox 0

NADred 0

Pi

ATP

0

ATP

0

1

0

0

0

0

ADP

0

0

1

0

0

0

NADox

0

0

0

1

0

0

NADred

0

0

0

0

1

0

Pi

0

0

0

0

0

1

G6P

1

1

-1

0

0

0

F6P

1

1

-1

0

0

0

FBP

1

2

-2

0

0

0

1

-1

0

0

0

1

-1

1

-1

1

1 DHAP

2

1 -

13BPG

2

1

3 PG

2

0

0

1

-1

1

2 PG

2

0

0

1

-1

1

PEP

1 2

0

0

1

-1

1

1

-1

0

0

0

-1

1

1

-1

1

1

-

GAP

2

1 PYr

2

This is Fig. 6.2. When the reactants are listed in this order, the components are Glc, ATP, ADP, NADox, NADred, and Pi. This means that when the concentrations of the last five are specified, the equilibrium compositions of the remaining reactants can be calculated without using equcalcrx.

330

Mathematica Solutions to Problems

6.4 The following reaction is carried out enzymatically at 298.15 K, pH 7, and 0.25 M ionic strength. ATP + glucose = glucose6phos + ADP The initial concentrations of ATP and glucose are 0.001 M. What is the equilibrium composition? Solve this problem using Mathematica in two ways. (BasicBiochemData2 has to be loaded) Use equcalcrx: First calculate the apparent equilibrium constant.

18973.7

equcalcrx [nt-, lnkr-,no-l :=Module [ {as, Ink}, (*nt=transposed stoichiometric number matrix lnkr=ln of equilibrium constants of rxs (vector) no=initial canposition vector*) ( *Setup* lnk=LinearSolve Int ,lnkrl ; as-Nullspace [ntI ; equcalcc [as,lnk,nol I

-6 -6 {7.20251 10 , 7.20251 10 , 0.000992797, 0.000992797)

These are the equilibrium concentrations of ATP, glucose, glucose6phos, and ATP. This problem can also be solved using NSolve. Since there are four unknown concentrations, there have to be four independent relations between these four unknowns. There is one equilibrium constant expression and three conservations equations, which we take here to be the conservation of adenosine, glucose entity, and phosphorus. NSolve[{cglucose6phos*cad~/(catp*cglucose)==l.9O*lOA4,catp+cad~==O.OOl,cg~ucose+cg~ucos e6phos==.001,cat~+cglucose6~hos==.OOl},{catp,cglucose,cglucose6phos,cadp~l -6 -6 {{cglucose -> -7.30778 10 , c a t p - > -7.30778 10 , cadp - > 0.00100731, -6 -6 cglucose6phos - > 0.00100731}, {cglucose -> 7.20251 10 , c a t p --> 7.20251 1 0 cadp -> 0.000992797, cglucose6phos -> 0.000992797)}

The first solution is impossible because concentratins have to be positive. The second solution agrees with that obtained using equcalcrx. 6.5 Calculate the apparent equilibrium constant for the net reaction for the first five reactions of glycolyis that is, reactions 6.6-1 to 6.6-5) using equation 6.1-6. Check this by simply using the net reaction. (BasicBiochemData has to be loaded) The stoichiometric number matrix is

TalsleForm[nu,TableHeadings> { {llglcll, lmatp","g6p1*, i*adpil, "f6p1*, "f 16bip", 'Idihydroxyacetonephos",llglyceraldehydephos'' 1, Automatic} I

Systems of Biochemical Reactions

glc atP 96P adP f 6P f16bip dihydroxyacetonephos glyceraldehydephos

1 -1 -1 1 1 0 0

0 0

331

2 3 4 5 0 0 0 0 0 - 1 0 0 - 1 0 0 0 0 1 0 0 1 - 1 0 0 0 1 - 1 0 0 0 1 1 0 0 1 1

The vector of standard transformed Gibbs energies of formation at pH 7 and is=0.25 M is v e c t o r O = { g l u c o s e , a t g , g l u c o s e 6 ~ h o s , a d g r f r r o x y a c e t o n e p h o s ,glyceraldehyBephos)/.gH->7/.is->.25

{-426.708, -2292.5, -1318.92, -1424.7, -1315.74, -2206.78, -1095.7, -1088.04)

The pathway vector is vectors={l,l,l,l,l); vectorG.nu.vectors

-29.105 apparentK=Exp[29.105/(8.31451*.29815)1

125581.

The net reaction is glc + 2ATP = 2dihydroxyacetonephos

+ 2ADP

calckprime[glucose+2*atg+de==2*dihydroxyacetonephos+2*adg,7,.251

125587.

’-,

6.6 A liter of aqueous solution contains 0.01 mol H2 PO4 - , 0.01 mol H P 0 , and 0.01 mol Mg2+. Assuming that the ionic strength is zero, what is the equilibrium composition of the solution in terms of species at 298.15 K? (BasicBiochemData has to be loaded) This problem canbe solved in two different ways. Using equcalcc, the conservation matrix with H, Mg, and P as components and H+,M g 2 + , Hz PO4 - , HPO, and MgHPO, as species is given by

‘-,

H 1

H M

P

g

O

0

Mg 0

H2P042

HP0421

MgHP04 1

1

0

0

1

0

1

1

1

332

Mathematica Solutions to Problems

The standard Gibbs energies of formation in kJ mol-'are used to construct Ink.

{O,

183.665, 458.779, 442.159, 632.065)

The initial composition matrix is given by noa=C0,.01,.01,.01,0}; (0,

0.01, 0.01, 0.01, 0 )

The amounts of the species at equilibrium (in the order used above) are given by equcalcc [as-,lnk-,no-l :=Module[ {l,x,b,ac,m,n,e,k}, ( * aseconservation matrix Ink=-(l/RT)(Gibbs energy of formation vector at T) nozinitial composition vector * ) (*setup*) (m,n}=Dimensions [as1; b=as no; ac=as; (*Initialize*) l=LinearSolve[ as.Transpose[asl,-as.(lnk+Log[nl) I ; ( *Solve* Do[ e=b-ac. (x=EA(lnk+l.as) ) ; If [ (lOA-lO)>Max[Abs [el I , Break[] I ; l=l+LinearSolve[ac.Transpose[as*Table~x,~m~~~,e~, Ck,10011; If [ k=lOO,Return[llAlgorithmFailed"] 1 ; Return [XI

.

I

equcalcc Caa, lnka,noal -7 11.70726 10 , 0.00354638, 0.00999983, 0.00354655, 0.00645362)

TableFonn[{egucalcc[aa,lnka,noa] },TableHeadings->{{"c/M"), ("H",11Mg",11H2P04-","HP042I*, "MgHP04ID 1 1 I

H

-7 1.70726 10

c/M

Mg

H2PO4-

HP042-

MgHP04

0.00354638

0.00999983

0.00354655

0.00645362

This problem can also be solved using the stoichiometric number matrix for the two reactions and equcalcrx H~ po0- = H+ + H P O ~2 K1= 6.05499*IO"-8 MgHP04- = Mg2++ HP04'Kz= 1.9489*10"-3 The transformed stoichiometric number matrix is given by

TableFornlEtnual 1 0

0 1

- 1 1 0 0 1 - 1

Systems of Biochemical Reactions

333

lnkra=Log[{6.05499*10A-8,1.9489*10A-311 {-16.6198,

-6.24049)

The initial amount vector is unchanged, and so the equilibrium composition is given by equcalcm t tnua, lnkra,noal {1.70726 1 0

-'I

, 0.00354638, 0.00999983, 0.00354656, 0.00645362)

TableForm[{equcalcm[tnua,lnkra,noal 1 ,TableHeadings->{{ " c / M " ) , 'I, "HP042-n, "MgHPO4 " 1 1 1 H

c/M

-7

1 . 7 0 7 2 6 10

{"H", " M g " , "H2P04-

Mg

H2P04-

HP04 2 -

MgHPO4

0.00354638

0.00999983

0.00354656

0.00645362

6.7 When 0.01 M glucose 6-phosphate is hydrolyzed to glucose and phosphate at 298.15 K in the pH range 9-10, only four species have to be considered. GlcP2-+ Hz 0 = Glc + HP04 What is the equilibrium composition assuming the ionic strength is zero?

'-

This calculation using equcalcc involves the problem that a, Go H2 0) is used in the calculation of the equilibrium constant K, but the expression for the equilibrium constant does not involve the concentration of Hz0. Thus in effect oxygen atoms are not conserved, because in dilute aqueous solutions they are drawn for th essentially infinite reservoir of the solvent. Therefore, the further transformed Gibbs energy G has to be used. The conservation matrix with C and P as components and GlcP2-, Glc, and HPOd2-asspecies is given by

TableForm[abl 6 1

6 0

0 1

The H row and charge row are redundant, and so they are omitted. The transformed Gibbs energy has to be used because the "concentration" of water is held constant. These transformed Gibbs energies of formation are given by tgeGlcP=-1763.94-9*(-237.19) 370.77

tgeGlc=-915.9-6*(-237.19) 507.24

tgeHPO4=-1096.1-4*(-237.19) -147.34

where the standard Gibbs energy of formaton of H 2 0 is -237.19 kJ m o l - l .

334

Mathernatica Solutions to Problems

{-149.566,

-204.627,

59.4359)

nob={0.1,0,01

{O.l, 0 , 0) equcalcc [ab,lnkb,nobl {0.000124334, 0.0998757,

0.0998757)

This problem can also be solved using the stoichiometric number matrix. Water is omitted from the stoichiometric number matrix, and so the transposed stoichiometric number matrix is given by tnub={{-l,l,l11; TableForm [ tnubl

-1

1

1

The transformed Gibbs energy of reaction is given by tgeGlc+tgeHPO4-tgeG1cP -10.87

lnkrb={(-1/(8.31451*.29815))*(-10.87)1 {4.38488)

equcalcrx [tnub,lnkrb,nobl {0.000124334, 0.0998757, 0.09987571

Thus the concentration of G6P2- is 1 . 2 4 x ~ O - ~ .

6.8 A liter of aqueous solution contains 0.02 mol phosphate and acid andNaCl are added to bring it to pH 7, and 0.2.5 M ionic strength. What is the equilibrium composition in terms of phosphate species? (BasicBiochemData2 has to be loaded) Since H and Mg are not conserved, the conservation matrix is as= C { 1,1,1) 1

{{I, 1, 1))

where the species are H2 PO4 - ,HP04 2 - , and MgHP04. The transformed Gibbs energies of these three species at 2.5 O C, pH 7, pMg 3, and I = 0.25 M have been calculated by Alberty and Goldberg (1992), and they can be used to calculate 1nk~-(1/(8.31451*.29815))*{-1056.58,-1058.57,-1050.441 {426.217, 427.02, 423.74)

The equilibrium concentrations of the three phosphate species are given by

Systems of Biochemical Reactions equcalcc[as,lnk,~0.01,0.01,0}] {0.00603194, 0.0134613, 0.000506736)

Alternatively, we can use the transposed stoichiometric number matrix

where the reactions are H2 PO4- = HP04’- K1= exp[(1058.57 - 1056.58)/RT] MgHPO,I=HP042- Kz= exp[(1058.57-1050.44)/RT] Thus lnkr is given by lnkr={(1058.57 {0.802752,

-

1056.58~/~8.31451*.29815),(1058.57-1050.44)~(8.31451*.29815)~

3.27959}

The equilibrium concentrations of the three species are the same as obtained using the conservation matrix. equcalcrxltrnu,lnkr, { O . 01,O. Ol,O} 3 {0.00603194, 0.0134613, 0.000506736)

33:

Chapter 7 Thermodynamics of Binding of Ligands by Proteins 7.1 Use the equilibrium constants in equations 7.1-3 to 7.1-6 to calculate the further transformed Gibbs energies of formation of the forms of the tetramer of hemoglobin and of the pseudoisomer group at O,]= 5 x ~ O - ~lo-', , and 2 x ~ O - ~ M(a). Make a table with the last three columns like Table 7.1. (b) Calculate the equilibrium mole fractions of forms of the tetramer at 21.4 OC, 1 bar, pH 7.4, (21-1 = 0.2 M, and 0.2 M ionic strength and make a table like Table 7.2.

7.2 Use the equilibrium constants in equations 7.3-2 and 7.3-3 to calculate the further transformed Gibbs energies of formaand 2 x ~ O - ~ M . tion of the forms of the dimer of hemoglobin and of the pseudoisomer group at O,] = 5 x ~ O - ~ , Make a table with the last three columns and first four rows of Table 7.3. 7.3 Calculate the fractional saturation Y, of the tetramer of human hemoglobin with molecular oxygen using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 "C, 1 bar, pH 7.4, [ C l - ] = 0.2 M and 0.2 M ionic strength. Make the calculation with the Adair equation and also by using the binding polymomial Y,. 7.4 Calculate the fractional saturation Y, of the dimer of human hemoglobin with molecular oxygen using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 "C, 1 bar, pH 7.4, [ C l - ] = 0.2 M and 0.2 M ionic strength. Make the calculation with the Adair equation and also by using the binding polymomial P, . 7.5 (a) Calculate the oxygen binding curve Y for human hemoglobin when the dimer and tetramer are in equilibrium using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 "C, 1 bar, pH 7.4, [ C l - ] = 0.2 M and 0.2 M ionic strength. This plot depends on the heme concentration. The currently accessible range of heme concentrations is about 0.04 pM to 5 mM. Plot logK" versus [O,].(b) Use the equation for Y to extrapolate to values of Y , at high heme concentrations. (c) Use the equation for Y to extrapolate to values of Y, at low heme concentrations.

337

338

Mathernatica Solutions to Problems

7.1 Use the equilibrium constants in equations 7.1-3 to 7.1-6 to calculate the further transformed Gibbs energies of formation and 2 xlO-'M. (a) of the forms of the tetramer of hemoglobin and of the pseudoisomer group at O z ] = 5 x ~ O - ~ , Make a table with the last three columns like Table 7.1. (b) Calculate the equilibrium mole fractions of forms of the tetramer at 21.4 OC, 1 bar, pH 7.4, Cl-]= 0.2 M, and 0.2 M ionic strength and make a table like Table 7.2.

(a) Calculate further transformed Gibbs energies of forms of the tretramer and the pseudoisomer group Ttot. calctgfT[ke~,conco2~]:=Module[{b,m,tgf,ge~nO2,gtrans,g~so,out~ut~,~*This program returns the standard further transformed Gibbs energies of formation of the forms of the tetramer of hemoglobin and the standard further transformed Gibbs energy of the pseudoisomer group at a specified molar concentration of molecular oxygen and specified equilibrium constants. keg_ is a vector of equilibrium constants. conco2 is the molar concentration of molecular oxygen.*) b=-1*(8.31451*10A-3)*294.65*Log[ke~li16.1; m=~~1.0,0,03,~-1.1,0,0~,~0,-1,1,0~,~0,0,-1,1~~; ge=LinearSolve[m,bl; tgf={Flatten[{O,ge}I}; n02=C{Oll,2,3,4~1; gtrans=Transpose[tgf]-Transpose[nO2l*(16.l+(8.3l45l*lOA-3)*294.65*Log~conco2l~; giso=-l*(8.31451*10A-3)*294.65*Log[Aggly[Plus,Exp[-gtrans/((8.31451*10A-3)*294.65~lll; output={gtrans,giso}; Return[output] I keq={43970.,12210.,404900.,664400.}; coll=Flatten[calctgfT[keq,5*10A-611;

co12=Flatten[calctgfT[keq,10A-511;

co13=Flatten[calctgfT[keq,2*10A-511;

TableForm[Transpose[{coll,col2,col3~l,TableHead~ngs> { { T n , "T( 02 ) I', " T ( 02 ) 2 " ,"T ( 02 ) 3 ' I , 'IT ( 02 ) 4 ' I , 'IAfG ' I o ( TOtT ) " } ,{ " 5x10 A - 6 M" ," 10 A - 5 M","2x10A-5 M " ) } l T

5~10"-6M 0

10A-5 M 0

2~10"-5M 0

"(02)

3.71109

2.01297

0.314846

T(02)2

10.5611

7.16484

3.76859

T(02)3

8.83313

3.73877

-1.3556

T(02)4

5.89189

-0.900589

-7.69307

AfG' 'O(T0tT)

-0.736508

-2.8149

-8.06907

(b) Calculate the equilibrium mole fractions of the various foms of the tetramer.

TableForm[Transpose[{colll,coll2,coll3~~,TableHead~ngs> { { "T","T(02) 'I, "T(02) 2 ' I , "T(02) 3 'I, 'IT (02) 4" } ,{ "5x10A 6 M" ," 10 A - 5 M" ,"2x10 A - 5 M" 1 1 1

-

Thermodynamics of Binding of Ligands by Proteins

T

5~10"-6M 0.740351

10A-5 M 0.316953

2x10A-5 M 0.0371174

T(02)

0.162766

0.139364

0.032641

T(02)2

0.00993687

0.0170164

0.00797093

T(02)3

0.0201172

0.0688993

0.0645486

T(02)4

0.0668293

0.457767

0.857722

339

7.2 Use the equilibrium constants in equations 7.3-2 and 7.3-3 to calculate the further transformed Gibbs energies of formation of the forms of the dimer of hemoglobin and of the pseudoisomer group at O,] = 5 x ~ O - ~ , and 2 xlO-'M. Make a table with the last three columns and first four rows of Table 7.3. calctgfD[ke~,conco2~]:=Module[{b,bl,b2,m,tgf,ge,nO2,gtrans,giso,out~ut},(*This program returns the standard frurther transformed Gibbs energies of formation of the forms of the dimer of hemoglobin and the standard further transformed Gibbs energy of the pseudoisomer group at a specified molar concentration of molecular oxygen and specified equilibrium constants. keg_ is a vector of equilibrium constants. conco2 is the molar concentration of molecular oxygen.*) b1=-1*(8.31451*10A-3)*294.65*Log[keq[[ll~l+l6.l+3O.O832; b2~-1*(8.31451*10"-3)*294.65*L0~~k~~[[2]11+16.1;

b={bl,b2);

{-1,1}3; ge=LinearSolve [m,bl ; tgf={Flatten[{30.0832,ge)l); n02={{0,1,2}); gtrans=Transpose[tgf]-Transpose[nO2]*(16.l+(8.3l45l*lOA-3)*294.65*Log[conco2]); giso=-1*(8.31451*1OA-3~*294.65*Log[A~~ly[P~us,E~[-gtrans/( (8.31451*10A-3)*294.65)lll; output={gtrans,giso); R€~tUrn[OUtpUtl]

m={{1,0),

keq={3.253*1OA6,8.155*lOA5);

co121=Flatten[calctgfD[keq,5*10A-611; co122=Flatten[calctgfD[keq,10A-511;

co123=Flatten[calctgfD[keq,2*10A-511;

Table 7.3 Standard further transformed Gibbs energies of formation of dimer at 21.5 C, pH 7.4, C1-]= 0.2 M and 0.2 M ionic strength Tab~eForm[Transpose[{col2l,co~~~,co~~~~],TableHeadings> { { "D","D(02) " ,"D(02) 2 " ,"A fG ' ' 0 (TotD) " } ,{ " 5x10 A - 6 M" ," 10 A - 5 M" ,"2x10A - 5 M" 1 1 1 D

5x10A-6 M 30.0832

10"-5 M 30.0832

2x10A-5 M 30.0832

D(02)

23.2505

21.5524

19.8542

D(02)2

19.8072

16.411

13.0147

A f G ' 'o(TotD)

19.2404

16.1194

12.8668

7.3 Calculate the fractional saturation YT of the tetramer of human hemoglobin with molecular oxygen using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 OC, 1 bar, pH 7.4, [ C l - ] = 0.2 M and 0.2 M ionic strength. Make the calculation with the Adair equation and also by using the binding polymomial Y, . kT1=4.397*10*4;

340

Mathematica Solutions to Problems kT2=1.221*10"4; kT3=4.049*10"5; kT4=6.644*10"5;

yT=(kT1*o2+2*kT1*kT2*o2"2+3*kTl*kT2*kT3*o2A3+4*kTl*kT2*kT3*kT4*o2A4)/(4*(l+kTl*o2+kTl*k T2*02*2+kTl*kT2*kT3*02"3+kT1*kTl*kT2*kT3*kT4*02~4) );

1

0.8-

0.6-

0.4-

0.2-

5 ~ 1 0 - ~ 0.00001

'

'0. ' O o O O l 5 '

'

0.O O O 0 6 ° 2

Plot[Evaluate[o2*D[Log[pT]/4,o2ll,{o2,lOA-8,2*lOA-5~,PlotRange-~~O,l~,~eS~ab~~> ( [ \ !\ (0\-2\)1 ",'I\ !\ (Y\-T\)"11 i

7.4 Calculate the fractional saturation Y, of the dimer of human hemoglobin with molecular oxygen using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 OC, 1 bar, pH 7.4, [ C l - ] = 0.2 M and 0.2 M ionic strength. Make the calculation with the Adair equation and also by using the binding polymomial P, .

Thermodynamics of Binding of Ligands by Proteins

341

kD1=3.253*10A6; kD2=8.155*10A5;

Plot [yD, { 02,0,5 * 10 A - 6 } , PlotRange-> { 0 ,1 } ,AxesLabel-> { 'I \ !\ ( O\-2 \ ) 1 'I,

'I

\ !\ (Y\-D\ ) 'I 1 1 ;

.---0.8-

[02

1x10-6

6

1 + 3 . 2 5 3 10

1

5~10-~

2x10-6

12

0 2 + 2 . 6 5 2 8 2 10

02

2

7.5 (a) Calculate the oxygen binding curve Y for human hemoglobin when the dimer and tetramer are in equilibrium using the equilibrium constants determined by Mills, Johnson, and Akers (1976) at 21.5 O C , 1 bar, pH 7.4, [ C l - I = 0.2 M and 0.2 M ionic strength. This plot depends on the heme concentration. The currently accessible range of heme concentrations is about 0.04 pM to 5 mM. Plot logK" versus [ O , ] . (b) Use the equation for Y to extrapolate to values of Y, at high heme concentrations. (c) Use the equation for Y to extrapolate to values of YD at low heme concentrations.

342

Mathematica Solutions to Problems

(a) The values of Y, and Y, are calclted as follows: kT1=4.397*10"4; kT2=1.221*10"4; kT3=4.049*10"5; kT4=6.644*10"5;

kD1=3.253*10"6; kD2=8.155*10"5;

The apparent association constant K"(2D=T)for human hemoglobin is given by k=(4.633*10"10)*(l+kTl*o2+kTl*kT2*o2A2+kTl*kT2*kT3*o2A3+kTl*kT2*kT3*kT4*o2A4)/( (l+kDl*o 2+kDl*kD2*02"2)"2); plot [Log[ 10,k] ,{02,0,2 * 10A 5 1 ,AxesLabel - > { 1 \ ! \ ( O\-2 \ ) 1 ' I ,

-

logK I

I'

11;

The dependence of Y on [heme] is given by

The fractional saturation Y at the highest possible hemoglobin concentration is given by: yhigh=y/.hme->5*lOA-3; plotlaplot [yhigh,{02,0,2*1OA-5),PlotRange->{O, 1),AxesLabel->{"[ \ ! \ (0\-2\)I

"," Y " 1 1 ;

Thermodynamics of Binding of Ligands by Protcins

343

Y

The fractional saturation at the lowest currently possible hemoglobin concentration is given by: ylow=y/.heme->4*10A-8; plot2=Plot[ylow,{o2,O,2*lOA-5},PlotRange-~{O,l},~esLabel-~~ii~\!\~O\~Z\~l","Y"~l;

Y

The fractional saturation at a heme concentration l/lOth of the lowest currently possible hemoglobin concentration is given by :

344

Mathematica Solutions to Problems

Y 1 0.8

0.6

0.4

0.2

-

5 ~ 1 0 - ~ 0'.0 0 0 0 1

'

0 .'00'0015 '

'

0'. 0000~021

Y

(b) Plot Y versus [heme]-.5 at high [heme] to obtain y T . Y is plotted versus x, where x = [heme]-.5 or [heme] = 1/x2. Clear [XI

~ ~ ~ ~ [ { y f ~ / . 0 2 - > ~ O " - 4 , ~ f n x / . o 2 - > 2 * 1 0 " - 5 , / . 0 2 - ~ 5 * 1 0 ~ - 6 , ~ f n ~ ~ . ~ ~ > 1 0 * - 6 } , {x, 0 , 2 0 0 0 } ,PlotRange->{O,1) ,AxesLabel->{"\!\ ( [hemel\ A - . 5 \ ) " I "Y''}] ;

Thermodynamics of Binding of Liganda by Proteins

345

Y

r

1

.

.

.

.

I

500

.

.

.

.

4

1000

.

.

,

,

I

,

.

1500

,

.

I

2000

[heme]-.5

This is Fig. 1 in R. A. Alberty, Biophys. Chem. 63, 189-132 (1997). (c) Plot Y versus [heme] a very low concentrations of heme to obtain Y, by extrapolation.

~~~~[~~/.02->10~-4,~/.02->2*10~-5,~/.02->10~-~,~/~O2->5*~0~~6,~/. >lo"- 7 1, {heme, 0,lO A -7 1 ,PlotRange-> { 0 ,1 1 ,AxesLabel > C 'I [heme1 I' ," Y " 1 1 i

-

2 ~ 1 0 - ~4 ~ 1 0 - ~ 6 ~ 1 0 - ~ 8 ~ 1 0 - ~ 1 x 1 0 - 7 This is Fig. 3 in R. A. Alberty, Biophys. Chem. 63, 189-132 (1997)..

[heme]

Chapter 8 Phase Equilibrium in Aqueous Solutions 8.1 (a) Calculate the the standard transformed Gibbs eneries for the reaction C02tot = C02(g) + H 2 0 at 283.15 K, 298.15 K, and 313.15 K at pHs 5 , 6, 7, 8, and 9 at ionic strength 0.25 M. (b) Plot the Henry's law constants versus pH from pH 2 to pH 12. 8.2 (a) Calculate the standard transformed Gibbs energies for the reaction C02tot = C02(g) + H20 at 298.15 K and pHs 5 , 6, 7, 8, and 9 for ionic strengths of 0, 0.10, and 0.25 M. (b) Plot the Henry's law constants versus pH from pH 3 to pH 9. (c) Plot logK, as a function of pH at three ionic strengths.

347

348

Mathematica Solutions to Problems

8.1 (a) Calculate the the standard transformed Gibbs eneries for the Reaction C02tot = C02(g) + H 2 0 at 283.15 K, 298.15 K, and 313.15 K at pHs 5, 6, 7, 8, and 9 at ionic strength 0.25 M. (b) Plot the Henry's law constants versus pH from pH 2 to pH 12. (a) Calculation of the standard transformed Gibbs energy of reaction:. The following program can be used to calculate the function of temperature, pH, and ionic strength that represents the standard transformed Gobbs energy of formation of a reactant. ca~cdGHT[speciesmat-] := Module[{dGzero, dGzeroT,dHzero,zi, nH, gibbscoeff,pHterm, istem,gpfnsp,dGfn,dHfn},(*This program produces the function of T (in Kelvin), pH and ionic strength (is) that gives the standard transformed Gibbs energy of formation of a reactant (sum of species) and the standard transformed enthalpy. The input speciesmat is a matrix that gives the standard Gibbs energy of formation at 298.15 K, the standard enthalpy of formation at 298.15 K, the electric charge, and the number of hydrogen atoms in each species. There is a row in the matrix for each species of the reactant. gpfnsp is a list of the functions for the transformed Gibbs energies of the species. The output is in the form {dGfn,dHfn}, and energies are expressed in kJ mol"-l. The values of the standard transformed Gibbs energy of formation and the standard transformed enthalpy of formation can be calculated at any temperature in the range 273.15 K to 313.15 K, any pH in the range 5 to 9, and any ionic strength in the range 0 to 0.35 m by use of the assignment operator(/.).*) {dGzero,dHzero,zi,nH}=Transpose[speciesmatl; gibbscoeff=9.20483*1OA-3*t-l.284668*lOA-S*tA2+4.95l99*lOA-8*tA3~ dGzeroT=dGzero*t/298.15+dHzero*(l-t/298.15); pHterm = nH*8.31451*(t/10O0)*Log[lOA-pH1; istermG = gibbscoeff*((ziA2) nH)*(is".5)/(1 + 1.6*isA.5); gpfnsp=dGzeroT pHterm - istermG; dGfn=-8.31~51*(t/100~)*Log[App~y[P~us,Exp[-l*gpfnsp/(8.3~~5~*(t/~~~~~~~]~; dHfn=-tA2*D[dGfn/t,tl ; {dGfn,dHfn}l

-

-

The program calctrGerx is readily modified to take a list of temperatures. calctrGerxT[eg_,pHlist_rislislist_l:},(*Calculates the standard transformed Gibbs energy of reaction in kJ molA-l at specified pHs, ionic strengths, and temperatures for a biochemical equation typed in the form atpt+h2ot+de==adpt+pit, where the functions include temperature (in K). The names of the reactants call the appropriate functions of pH, ionic strength, and temperature. pHlist, islist, and tlist can be lists. This program can also be used to calculate the standard transformed enthalpy of reaction.*) energy=Solve [eq,del ; energy[[l,l,2ll/.pH->pHliSt/.is->islist/.t->tlist]

co2gt=calcdGHT[co2gspl~~lll

-0.00831451 t Log[E

(-120.272 (-393.5 ( 1

-

0.00335402 t)

-

1.32269 t))/t

I

co2tott=calcdGHT[co2totspl~[lll

-0.00831451 t Log[Power[E, (-120.272 (-677.14 (1 0.5 2 (0.00920483 t - 0.0000128467 t (4 is Power[E, (-120.272 (-699.63 (1 - 0.00335402 t) 0.5 2 (2 i s (0.00920483 t - 0.0000128467 t E

0.00335402 t) - 1.77028 t -8 3 0.5 + 4.95199 10 t ))/(1 + 1.6 is ) - 2.08992 t + -8 3 0.5 + 4.95199 10 t ))/(1 + 1.6 is )

(-120.272 (-691.99 (1 - 0.00335402 t) - 1.96804 t

-

0,00831451 t Log[lO-pHI))/t

1

) )

Phase Equilibrium in Aqueous Solutions

- 0 . 0 0 8 3 1 4 5 1 t Log[Power[E, ( - 1 2 0 . 2 7 2 ( 2 is

0.5

349

(1 - 0 . 0 0 3 3 5 4 0 2 t) - 0 . 7 9 5 5 3 9 t + 2 -8 3 0.5 (0.00920483 t - 0.0000128467 t + 4.95199 1 0 t ))/(1 + 1.6 is )

{{-6.8368, -8.24314, 13.03905, 2.57555,

(-285.83

-9.64371}, {-5.7574, -6.94646, -8.1138}, 2.12561}, 18.67202, 8.60993, 8.59301}}

I-2.12304,

-2.91737,

-

-3.65

TableForm [Transpose[ tab11 ,TableHeadings->{ { "283.15 K" ,"298.15 K" ,"313.15 K" 1, { "pH 511,18pH 6",I1pH 7","pH 8","pH 911))1 PH 5 -6.8368

PH 6

-5.7574

PH 7 -2.12304

PH 8

283.15 K

3.03905

PH 9 8.67202

298.15 K

-8.24314

-6.94646

-2.91737

2.57555

8.60993

313.15 K

-9.64371

-8.1138

-3.6971

2.12561

8.59301

The standard transformed Gibbs energy of reaction becomes more negative at lower pH and higher temperatures. (b) Plot the Henry's law constants at the three temperatures versus pH. plot283=Plot [Exptca1ctrOerxT[co2tott+de==co2gt+h2ot,pH,.25,283.15]/(8.31451*.28315)],{pH,2,12~,Dis~1ay~ nction->Identity]; plot298=Plot[Exp Ica1ctrGerxT[co2tott+de==co2gt+h2ot,pH,.25,298.151/(8.31451*.29815)1,~pH,2,12~,Disp1ay~ nction->Identity]; plot313=Plot CEXptca1ctrGerxT[co2tott+de==co2gt+h2ot,pH,.25,313.151/(8.31451*.31315)1,{~H,2,12~,Disp1ayFu nction->Identity]; \ !\ ( K\-H\ ) 1 ,Di splayFunct ion Show [plot28 3,plot 298, plot 3 13,Axe sLabel- > { lqpH1l, >$DisplayFunctionl;

350

Mathernatica Solutions to Problems

This is the equilibrium pressure in bars for an ideal 1 M solution of carbondioxide as a function of temperature. The equilibrium pressure increases with the temperature. This is Fig. 8.1. 8.2 (a) Calculate the standard transformed Gibbs energies for the reaction C02tot = C02(g) + H 2 0 at 298.15 K and pHs 5 , 6,7, 8, and 9 €or ionic strengths of 0, 0.10, and 0.25 M. (b) Plot the Henry's law constants versus pH from pH 3 to pH 9. (c) Plot logK,as a function of pH at three ionic strengths. (BasicBiochemData2 has to be loaded)

(a) Calculation of the standard transformed Gibbs energy of reaction:. calctrGerx[e~,pHlist_,islist_l:=Module[{energy},(*Calculates the standard transformed Gibbs energy of reaction in kJ molA-1 at specified p H s and ionic strengths for a biochemical equation typed in the f o m atp+hao+de==adp+pi. The names of the reactants call the appropriate functions of pH and ionic strength. pHlist and islist can be lists. This program can be used to calculate the standard transformed enthalpy of reaction by appending an h to the name of each reactant.*) energy=Solve [eq,deI; energy~[l,l,2]]/.pH->pH~~St/.iS->is~~St]

TableForm [Transpose[ tab11 ,TableHeadings-> { { m l I = O 1 l , "I=O.1" ," I = O . 25 1, E "pH 5", " p H 6", I'pH 7","pH 8","pH 9 " ) ) 1 'I

I=O

PH 5 -8.33561

PH 6 -7.55317

PH 7 -4.30451

PH 8

0.952641

PH 9 6.71138

I=O.1

-8.27119

-7.11762

-3.26789

2.17395

8.11334

I=O.25

-8.24314

-6.94648

-2.9174

2.57552

8.60988

The standard transformed Gibbs energy of reaction becomes more negative at lower pH and lower ionic strengths. (b) Plot the Henry's law constants at the three ionic strengths versus pH. Plot [hraluateCExp Cca1ctrGerx[co2tot+de==co2g+h2o,pH,{0,.1,.25~1~~8.31451*.29815~1,~pH,3,9~,~esLab~~> { '*pH", !\ (K\-H\) 'I 1 I 1 ; KH

Phase Equilibrium in Aqueous Solutions

351

The upper curve is for zero ionic strength. This is Fig. 8.2.

(c) Plot logK,as a function of pH at three ionic strengths. Plot [Evaluatef-

ca1ctrGerx[co2tot+de==co2g+h2o,~H,{0,.1,.25~1/~8.31451*.29815*Log~101~1,~PH,3,11~~~~S rigin-> {3, - 5 ) ,AxesLabel-r pH", 'I\ !\ (K\LH\)" 1 I ;

t

4

6

8

10

Note that the greatest effects of raising the ionic strength are at the highest pHs.

PH

Chapter 9 Redox Reactions 9.1 Calculate the standard apparent reduction potentials for 298.15 K at pHs 5, 6, 7, 8, and 9 and ionic strengths 0,0.10, and 0.25 M for the following biochemical half reactions and plot their pH dependencies at 0.25 M ionic strength. (1) O2 (aq) + 4 e - = 2 H 2 0 (2) O2 (8) + 4 e - = 2H20 (3) O2 (aq) + 2 e - = 2H2O2 (4) O2 (8) + 2 e - = 2H202 ( 5 ) cytochrome cox+ e - =cytochrome cred (6) pyruvate + 2 e - = lactate (7) acetaldehyde + 2 e - = ethanol (8) FMN,, + 2 e - z Fm,,d (9) retinal + 2e-= retinol (10) acetone + 2 e - = 2-propanol (11) NAD,, + 2 e - = NADred (12) NADP,, + 2 e - = NADP,,, (13) f erredoxin,, + e-= f erredoxin,,d (14) acetylcoA + 2e-= coA + acetaldehyde (15) 2e-= H2 (g) (16) 2e-= H2 (aq) 9.2 Calculate the apparent equilibrium constants K at 298.15 K and pHs 5,6, 7, 8, and 9 for the following four reactions and plot the base 10 logarithm of K versus pH: (1) N2 (8) + 8 ferredoxinred= 2 ammonia + H2 (g) + 8 ferredoxin,, (2) N2 (aq) + 8 ferredoxinred = 2 ammonia + H2(aq) + 8 ferredoxin,, (3) 2 ferredoxinred= H2 (8) + 2 ferredoxin,, (4) 2 ferredoxinred= H2 (aq) + 2 ferredoxin,, Note the ionic strength is not mentioned because the reference reactions and the dissociation of NH4 do not depend on the ionic strength. Note that the apparent equilibrium constaants of the first two reactions change by a factor of 10 when the pH is changed 0.10 in the neutral region. +

9.3 Calculate the standard apparent reduction potentials of the following half reactions involving carbon dioxide at 298.15 K, pHs 5, 6, 7, 8, and 9 and ionic strengths of 0, 0.10, and 0.25 M and plot them versus pH at ionic strength 0.25 M. (1) C 0 2tot + 2e- = formate + H20 (2) C 0 2(g) + 2e- = formate (3) COztot +pyruvate + 2 e - = malate + H20 (4) COz(g) +pyruvate + 2e- = malate (5) C 0 2tot + acetylCoA + 2e- = pyruvate + CoA + H20 9.4 Calculate the change in binding of hydrogen ions in the following 10 biochemical half reactions at 298.15 K, pHs 5, 6, 7, 8, and 9 and ionic strengths of 0, 0.10, and 0.25 M. Plot the change in binding at ionic strength 0.25 M versus pH. (1) C 0 2tot + 2e-= formate + H20 (2) C02 tot + acetyl-CoA + 2e-= pyruvate + CoA + H20 (3) ketoglutarate + ammonia +2e- = glutamate + H20 (4) pyruvate + ammonia +2e- = alanine + H20 (5) pyruvate + C 0 2tot + 2e-= malate + H20 (6) cystine + 2 e - = 2 cysteine + H2 (7) citrate + CoA + 2 e - = malate +acteyl-CoA + H20

353

354

Mathernatica Solutions to Problems

(8) o 2 ( g ) + 4 e - = 2 H z O (9) NAD,,+ 2e-= NADred (10) N2(g) + 8e-=2 ammonia + H,(g)

9.5 Plot the change in binding of hydrogen ions versus pH at ionic strength 0.25 M for the following five biochemical reactions: (1) NAD,, + formate + H20 = NADred + COztot (2) NAD,, + malate + H20 = NADred + C 0 2tot + pyruvate (3) NAD,, + ethanol = NADred + acetaldehyde (4) NAD,, + alanine + H20 = NADred + pyruvate + ammonia ( 5 ) NAD,, + malate + acetylcoA + H20 = NADred + citrate + coA

Redox Reactions

355

9.1 Calculate the standard apparent reduction potentials for 298.15 K at pHs 5 , 6 , 7, 8, and 9 and ionic strengths 0, 0.10, and 0.25 M for the following biochemical half reactions and plot their pH dependencies at 0.25 M ionic strength. 0, (aq) + 4 e - = 2H20 0, (8) + 4 e - = 2H20 O2 (sq)+ 2 e - = 2H2 O2 o2(g) + 2 e - = 2H2O2 cytochrome cox+e - = cytochrome cred pyruvate + 2 e - = lactate acetaldehyde + 2 e - = ethanol Fm,, + 2 e - z FMNred retinal + 2 e - = retinol (10) acetone + 2e- = 2-propanol (1 1) NAD,, + 2 e - = NADred (12) NADP,, + 2e-=NADPred (13) f e r r e d o x i n , , + e-= f e r r e d o x i n r e d (14) acetylcoA + 2e-= coA + acetaldehyde (15) 2 e - = H2 (8) (16) 2e-= H2 (aq) (BasicBiochemData has to be loaded) calcappredgot [ e L , nu-, pHlist-, islist-] := Module[{energy), (*Calculates the standard apparent reduction potential of a half reaction at specified ~ H Sand ionic strengths for a biochemical equation typed in the form nadox+de==nadred. The names of the reactants call the corresponding functions of p H and ionic strength. nu is the number of electrons involved. pHlist and islist can be lists.*) energy = Solve [eq, de] ; (-l*energy[[l, 1, 211 / (nu*96.485)) /. pH-ipHlist /. is-iislist

1

TableFonn[Transpose[calcapgredpot[nadox+de == nadred, 2, ( 5 , 6, 7, 8 , 9 } , {0, .l, .25}]], . Mml}, TableHeadings + { { "I=O M I 1 , "I=O.10 M I ' , l l I ~ O 25 { " p H 5 " , "pH 6" "pH 7 " , "pH 8 " , "pH 9")}, TableSpacing+ {I, I}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.265275 -0.294855 -0.324435 -0.354015 -0.383595

1 ~ 0 . 1 0M

-0.258932

-0.288512

-0.318092

-0.347672 -0.377252

1 ~ 0 . 2 5M

-0.256884

-0.286464

-0.316044

-0.345624

-0.375204

plot11 = Plot [calcappredpot [nadox+de== nadred, 2, pH, .25], { p H , 5, 9 } , AxesLabel + ( I 1 p H I m , l l E i o / V n } ] ;

356

Matheniatica Solutions to Problems

-0.26h -0.281

\ 6

\

7

8

9 PH

-0.32-0.34.

-0.36-

TableForm[Transpose[calcappredpot[nadpox+de == nadpred, 2, {5, 6, 7, 8, 9 ) , {0, .l, .25}]], O **I=O.lOMI', "1=0.25 M I ' } , TableHeadings + { { m * I ~M", {"pH 5 " , "pH 6 " , "pH 7 " . "pH 8 " , "pH 9")), Tablespacing-, {1, l}]

1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.282584 -0.312164 -0,341744 -0.371324 -0.400904

I=0.10 M

-0.263553 -0.293133 -0.322713 -0.352293 -0.381873

I=O.25 M

-0.257409 -0.286989 -0.316569 -0.346149 -0.375729

plot12 = Plot [calcappredpot[nadpox + de ::nadpred, 2, pH, .25], {pH, 5, 9}, AxesLabel + {llpH"," E ' ' /V")];

E '"/V

-0.

-0. -0. -0. -0. TableForm[Transpose [calcappredpot[02g + de ::2 * h20, 4, { 5, 6, 7, 8, 9}, { 0, .l, .25)] 1 , TableHeadings + { { "I=O M I 1 , "I=O.lO M", "I=0.25 M"), {"pH 5 " , "pH 6", "pH 7 " , "pH 8 " , 'lpH 9"}}, TableSpacing+ (1, l}]

1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 0.933355 0.874195 0.815036 0.755876 0.696716

I=O.lO M

0.927012 0.867852 0.808692 0.749532 0.690372

I=O.25 M

0.924964 0.865804 0.806644 0.747484 0.688324

plot2 = Plot[calcappredpot[o2g+de =: 2*h20, 4, pH, .25], {pH, 5, 9), AxesLabel-, {"pH", " E t 0 / V " ) ] ;

Redox Reactions

357

E '"IV

TableForm[Transpose[calcappredpot[o2aq+de=: 2*h20, 4 , (5, 6, 7, 8, 9 } , {O, .l, .25}]], TableHeadings -t { ( 1 1 1 = 0M", lnI=O.10M I 1 , "I=0.25 M " ) , ("pH 5 " , "pH 6", "pH 7 " , "pH el1, "pH 9 " } } , Tab1eSpacing-t {I, I}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 0.975849 0.916689 0.857529 0.798369 0.739209

I=O.lO M

0.969505 0.910345 0.851186 0.792026 0.732866

I=O.25 M

0.967457 0.908297 0.849138 0.789978 0.730818

plot1 = Plot[calcappredpot[o2aq+de =: 2*h20, 4, pH, .25], {pH, 5, 9 1 , AxesLabel

-f

{mlpH1l, llEto/V"}]i

E '"IV

TableForm[Transpose[calcappredpot[o2g+de::h202aq, 2, ( 5 , 6, 7, 8, 9 ) , {0, .l, .25}]], TableHeadings -t {{I1I=0M I q , "I=O.lO M I i , "I=0.25 M I ' } , {"pH 5 " , "pH 6", "pH 7", I'pH 8 " , "pH 9 * * ) } , Tab1eSpacing-t (1, l)]

I=O M

PH 5 PH 6 PH 7 PH 8 PH 9 0.398764 0.339605 0.280445 0.221285 0.162125

I=O.lO M

0.392421 0.333261 0.274101 0.214941 0.155781

I=O.25 M

0.390373 0.331213 0.272053 0.212893 0.153733

plot4 = Plot[calcappredpot[o2g+de

h202aq, 2, pH, .25], {pH, 5, 9 ) , AxesLabel

: :

-f

{"pH", "Eta / V " ) I ;

358

Mathematica Solutions to Problems

E '"/V

TableForm[Transpose[calcappredpot[o2aq+de == h202ag, 2, {5, 6, 7, 8 , g } , { o r .I, .25)]] TableHeadings -f { { " I = O M", " I = O . 10 MI', " I = O . 25 M" } , {"gH 5", "pH 6", "gH 7 " , "gH 8", l1pH 9"}}, TableSgacing-t {l, I}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 0.483752 0.424592 0.365432 0.306272 0.247112

I=O.lO M

0.477408 0.418248 0.359088 0.299928 0.240769

I=O.25 M

0.47536

0.4162

0.35704

0.29788 0.238721

plot3 = Plot [calcaggredgot[olaq + de =: h202ag, 2, gH, .25], {gH, 5, 9}, AxesLabel

-t

{ tlpH1l, " E I /V" 1 I

Calcappredpot fails when the oxidized and reduced forms contain the same number of hydrogen atoms. In this case, there is no pH dependence, and the standard apparent reduction potential can be calculated by using ~-1/96.485~*(cytochromecred-cytochromecox/.is-~{0,.1,.25})

{0.254029, 0.222311, 0.212071)

Redox Reactions

359

17

0.80.6-

0 0

6

7

8

9

TableForm [ Transpose[calcappredpot[acetaldehyde+de == ethanol, 2, (5, 6, 7, 8, 9}, {0, .l, .25}]], TableHeadings -+ {{"I=O M", "I=O.lO MI', "I=0.25 MI'}, {"pH 5 " , "pH 6 " , "pH 7", I1pH 8", "gH 9 " } } , TableSpacing-) (1, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.0748325 -0.133992 -0.193152 -0.252312 -0.311472

1~0.10M

-0.0811761 -0.140336 -0.199496 -0.258656 -0.317816

I=O.25 M

-0.0832242 -0.142384 -0.201544 -0.260704 -0.319864

plot7 = Plot [calcappredpot[acetaldehyde+ de =: ethanol, 2, pH, -251 , {pH, 5, 91, AxesLabel -+ { llpHml, I I E l o/V'l)] i

TableForm[Transpose[calcappredpot[frnnox+de== fmnred, 2, ( 5 . 6, 7, 8, 9 } , ( 0 , .I, . 2 5 ) ] ] , TableHeadings + { {111=0 M", llI=O.10MI1, "I=0.25 M"}, {"pH 5 " . "pH 6 " , "pH 7", llpH8", "pH 9 * I ) ) , Tablespacing-+ {I, I}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.0943174 -0.153477 -0.212637 -0.271797 -0.330957

1 ~ 0 . 1 0M

-0.100661

-0.159821 -0.218981 -0.278141 -0.337301

1 ~ 0 . 2 5M

-0.102709

-0.161869 -0.221029 -0.280189 -0.339349

plot8 = Plot [calcappredpot[fmnox + de == fmnred, 2, pH, -251, {pH, 5, 9 ) , AxesLabel -+ {"pH", l l E 1 o / V g l } ] ;

360

Mathematica Solutions to Problems

TableFom [ Transpose[calcappredpot[pyruvate+de==lactate, 2, (5, 6, 7, 8, g } , TableHeadings + { {*'I=OM " , "1=0.10 M", "1=0.25 M"}, {"pH 5", "pH 6'1, I1pH 7 " , ''pH 8 " , ''pH S i r } } , Tablespacing-, (1, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.0654528 -0.124613 -0.183773 -0.242932 -0.302092

1 ~ 0 . 1 0M

-0.0717964 -0.130956 -0.190116 -0.249276 -0.308436

I=O.25 M

-0.0738445 -0.133004 -0.192164 -0.251324 -0.310484

{o, .1, .25}]],

plot6 = Plot [calcappredpot[pyruvate+ de =: lactate, 2, RH, .25], {pH, 5, 9}, AxesLabel -B { mlpH1l, " E / V l } ];

\

-0.251

1

6

7

8

'9

PH

TabbFom[Transpose[calcappredpot[de:=h2g, 2, {5, 6, 7, 8, 9 } , (0, .l, .25}]], TableHeadings + { { I I I = O M I 1 , llI=O.10M", "1=0.25 M"}, {"pH 5 " , "pH 6 " , "pH 711,"pH Err, "pH 9 " } } , Tablespacing -t 11, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH. 9 -0.295799 -0.354959 -0.414119 -0.473279 -0.532439

I=0.10 M

-0.302143 -0.361303 -0.420463 -0.479623 -0.538783

I=O.25 M

-0.304191 -0.363351 -0.422511 -0.481671 -0.540831

plot15 = Plot [calcappredpot[de == h2g, 2, pH, .25], {pH, 5, 93, AxesLabel + { i s p H " , " E

/V"}l;

l o

Redox Reactions

361

E '"/V

TableForm[Transpose[calcappredpot[de== h2aq, 2, (5, 6, 7, 8, 9 ) , {0, -1, .25)]], TableHeadings + { {"I=O M I 1 , "I=O.lO ME', "I=0.25 M"}, {"pH 5", "pH 6", "pH 7 " , "pH 8 " , "pH 9 " } } , Tablespacing-, {I, l}] 1=0 M

PH 5

PH 6 PH 7 PH 8 PH 9 -0.387005 -0.446165 -0.505325 -0.564485 -0.623645

I=O.10 M

-0.393349 -0.452509 -0.511669 -0.570829 -0.629989

I=O.25 M

-0.395397 -0.454557 -0.513717 -0.572877 -0.632037

E '"/V

-0.. 5. -0.55-

6

7

8

9\

pH

Since neither ferredoxinox or ferredoxinred contains hydrogen atoms, the pH-dependent apparent reduction potential is calculated using ~-1/96.485~*~ferredoxinred-ferredoxinox/.is-~{O,.l,~25}) I-0.394569, -0.400913, -0.402961}

362

Mathematica Solutions to Problems

10.75~

0.5-

0.25!

-0.25-

6

7

8

9

-0.51 I

-0.75

-1

t

TableForm[Transpose[calcaggredpot[retinal+de::retinol, 2, {5, 6, 7, 8, 9), { O , .1, .25}]], TableHeadings -+ {{"I=O M", "I=O.lO M", "I=0.25 MI'}, ( " p H 5". "pH 6", "pH 7 " , "pH El1, "pH 9"}}, Tablespacing- 11, l}] 1=0 M

PH 5

PH 6 PH 7 PH 8 PH 9 -0.151166 -0.210325 -0.269485 -0.328645 -0.387805

1~0.10M

-0.157509 -0.216669 -0.275829 -0.334989 -0.394149

1 ~ 0 . 2 5M

-0.159557 -0.218717 -0.277877 -0.337037 -0.396197

plot9 = Plot [calcappredpot[retinal + de ::retinol, 2, pH, -251, { p H , 5, 9}, AxesLabel -+ {mlpHmm, " E i 0/V"} I ;

E '"/V

TableFom [ Transpose[calcappredpot[acetone+de:-propanol2, 2, (5, 6, 7, 8, 93, { O , .l, .25}]], TableHeadings -+ { {''I=O MI', llI=O.10M". "I=0.25 M"), ("pH 5", " p H 611, "pH 7 " , "pH 8", "pH 9"}}, TableSpacing- {l, l}]

1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.163499 -0.222659 -0.281819 -0.340979 -0.400139

1~0.10M

-0.169843 -0.229003 -0.288162 -0.347322 -0.406482

1~0.25M

-0.171891 -0.231051 -0.290211 -0.34937 -0.40853

plot10 = Plot [calcappredpot [acetone + de == propanola, 2, pH, .25], { p H , 5, 9}, AxesLabel + { " p H r r , " E 1 o/V"}I i

Redox Reactions

E '"/V

TableForm [Transpose[ calcappredpot[acetylcoA+de ==coA+acetaldehyde,2, {5, 6, 7, 8, 9}, {0, .l, .25}]I , TableHeadings + { { " I = O M", "I=O.lO Mi', "I=0.25 M I i } , {"pH 5", '*pH 6 " , "pH 7 " , **pH8", "pH S t # } } , TableSpacingj {I, l}] 1=0 M

PH 5 ??H 6 PH 7 PH 8 PH 9 -0.262266 -0.321377 -0.380065 -0.435269 -0.477795

1~0.10 M

-0.268606 -0.327687 -0.386084 -0.439399 -0.4788

I=O.25 M

-0.270652 -0.32972

-0.387991 -0.440576 -0.479044

plot14 = Plot [calcappredpot[acetylcoA + de == coA + acetaldehyde, 2, pH, .25], {BH, 5, 9}, AxesLabel -t {''pHin, i w E t o / V i i } ] ;

Show[ {plotl, plOt2, plot3, plot4, plots, plOt6, plot7, plot8, plOt9, plotlo, plOt11, plOt12, plotl3, pl0tl4, plOtl5, plOtl6) I Axesorigin-> { 5 , - . 8 } , AspectRatioj1.5, PlotRangej { - . 8 , I}];

363

364

Mathematica Solutions to Problems

-------

I

-0.75

6

7

8

9

9.2 Calculate the apparent equilibrium constants K' at 298.15 K and pHs 5, 6, 7, 8, and 9 for the following four reactions and plot the base 10 logarithm of K' versus pH: (1) N2 (8) + 8 ferredoxinred= 2 ammonia + H2(g) + 8 ferredoxin,, (2) N2 (aq) + 8 ferredoxinred= 2 ammonia + H2(aq) + 8 ferredoxin,, ( 3 ) 2 ferredoxinred= H2(8) + 2 ferredoxin,, (4) 2 ferredoxinred= H2(aq) + 2 ferredoxin,, Note the ionic strength is not mentioned because the reference reactions and the dissociation of NH4 do not depend on the ionic strength. Note that the apparent equilibrium constants of the first two reactions change by a factor of 10 when the pH is changed 0.10 in the neutral region. +

(BasicBiochemData2 has to be loaded) These calculations and plots can be made by using the program calckprime.

Redox Reactions

365

31 21 11 -9 {1.39705 10 , 1.39846 10 , 1.41258 10 , 15.5771, 3.39921 10 }

Note that the apparent equilibrium constants decrease by a factor of 10" per pH unit and becomes non-spontaneous just above pH 8 Plot [Log[ 10, kprimel ] ,{pH, 5,9 } ,AxesLabel - > { "pH", log K ' 'I 1 1 ;

log K '

kprime2/.pH->{5,6,7,8,91

31 21 11 -9 {2.17732 10 , 2.17951 10 , 2.20152 10 , 24.2771, 5.29772 10 }

log K'

kprime3=calckprime[2*ferredoxinred+de==h2g+2*ferredoxinox,pH,.251; kprime3/.pH->{5,6,7,8,9}

{2183.11, 21.8311, 0.218311, 0.00218311, 0.0000218311) Plot [Log110,kprime3 1, {pH, 5,9}, AxesLabel-> { "pH", "log K' 'I 1 I

;

366

Mathematica Solutions to Problems

log K'

-6

I1.8018, 0.018018, 0.00018018, 1.8018 10

-8

, 1.8018 10

}

Plot [Log[I0,kprime4],{pH, 5,9} ,AxesLabel->{ "pH", "log K' "> 1 ;

log K'

9.3 Calculate the standard apparent reduction potentials of the following half reactions involving carbon dioxide at 298.15 K, pHs 5, 6, 7, 8, and 9 and ionic strengths of 0, 0.10, and 0.25 M and plot them versus pH at ionic strength 0.25 M. (1) COz tot + 2 e - = formate + H20 (2) C02 (g) + 2 e - = formate (3) C 0 2tot +pyruvate + 2e- = malate + H2 0 (4) C 0 2(g) +pyruvate + 2e- = malate ( 5 ) C 0 2tot + acetylCoA + 2e- = pyruvate + CoA + H20

(BasicBiochemData2 has to be loaded) calcappredpot [ e e l nu-, pHlist-, islist-] := Module [ {energy}, (*Calculates the standard apparent reduction potential of a half reaction at specified pHs and ionic strengths for a biochemical equation typed in the form nadox+de==nadred. The names of the reactants call the corresponding functions of p H and ionic strength. nu is the number of electrons involved. pHlist and islist can be lists.*) energy Solve [eq, de] ; (-l*energy[[l, 1, 211 / (nu*96.485)) /. pH-pHlist /. isjislist

1

Redox Reactions

367

TableForm [ Transpose[calcappredpot[co2tot+de:: formate+h20, 2, { 5 , 6, 7, 8, 9}, {0, -1, .25}]]. Tab1eHeadings-t {{"I=O M I 1 , llI=O.10M", ''I=O.25 MI'], { " p H 5 " , "pH 6", "pH 7", "pH 8", " p H 9 " } } , Tab1eSpacing-t (1, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.329401 -0.363036 -0.409451 -0.466274 -0.525697

I=O.lO M

-0.329735 -0.365293 -0.414823 -0.472603 -0.532962

I=O.25 M

-0.329881 -0.36618

-0.416639 -0.474684 -0.535535

plot1 = Plot [calcappredpot[coltot+ de =: formate + h20, 2, g H , .25], { p H , 5, 9 } , AxesLabel -t { " p H t l , "Era / V " ) l ;

The chemical reaction corresponding with reaction 2 is not affected by ionic strength because z i = NH,and so the table of apparent reduction potentials can be made more simply; calcappredpot [co2g+de==formate, 2

{ 5,6,7,8,9),

.251

{-0.372598, -0.402178, -0.431758, -0.461338, -0.490918)

plot2

Plot [calcappredpot[co2g+ de =- formate, 2, pH, .25]8

{ p H , 5, 9 } , AxesLabel + { l n p H B @l, l E 1 o / V 1 l } ] ;

-0

-0

-0 -0 -0

TableForm [Transpose[ calcappredpot [pyruvate+ co2tot + de == malate + h20, 2, { 5, 6, 7, 8, 9 } , { 0, .l, .25}] 1 , TableHeadingsj {{"I=O M", lmI=O.10MI'. "I=0.25 M a n ) , { " p H 5". "pH 6", "pH 7", " p H 8 " , "pH 9 " ) } , Tab1eSpacing-t {I, l}]

368

Mathernatica Solutions to Problems PH 7 PH 8 PH 9 -0.308738 -0.365769 -0.425213

1=0 M

PH 5 PH 6 -0.215617 -0.26041

1~0.10M

-0.216271 -0.257627 -0.307911 -0.365769 -0.426136

1 ~ 0 . 2 5M

-0.215868 -0.25669

-0.307703 -0.365804 -0.426661

plot3 = Plot [calcappredpot[pyruvate+ co2tot + de == malate {pH, 5, 9 } , AxesLabel + {"pH", "El"/V,'I 1 i

+ h20, 2,

pH, . 2 5 ] ,

TableForm [ Transpose[calcappredpot[pyruvate+co2g+de::malate8 2, {5, 6, 7, 8, 9}, {0, .l, .25)]], TableHeadings -f {{.I=O M I 1 , "I=O.lO MI', "I=0.25 MI'}, {"pH 5", "pH 6 " , "pH 7", "pH El', llpH9 " ] ] , Tab1eSpacing-t {I, l}] 1=0 M

PH 5 PH 6 PH 7 PH 8 PH 9 -0.258813 -0.299552 -0.331045 -0.360832 -0.390433

1 ~ 0 . 1 0M

-0.259134 -0.294511 -0.324846 -0.354503 -0.384091

I=O.25 M

-0.258585 -0.292687 -0.322821 -0.352458 -0.382043

plot4 = Plot [calcappredpot[pyruvate+ co2g + de =: malate, 2, pH, -251, {pH, 5, 91, AxesLabel + {llpH1m, m m E/V") io I:

TableForm [Transpose[calcappredpot[ acetylcoA + co2tot + de =: COA + pyruvate + h20, 2, {5, 6, 7, 8, 91, { 0, .l, .25}] 1, TableHeadings + { { "I=O MI', " I = O . 10 M", "I=O.25 M",], {"pH 5", "gH 6 * * , "pH 7", "pH 8 " , "pH 9 " } ] , Tablespacing+ {I, l}]

Redox Reactions

1=0 M

PH 5 -0.387747

PH 6 PH 7 PH 8 PH 9 -0.421334 -0.467277 -0.520144 -0.562932

1 ~ 0 . 1 0M

-0.388078

-0.423557

-0.472324

-0.524259

1 ~ 0 . 2 5M

-0.388221

-0.424428

-0.473999

-0.525469 -0.565628

plot5

Plot [calcappredpot[acetylcoA + co2tot

{ p ~ 5, , 9}, a e s L a b e l + { ~ ~ p1 ~1 i ~ /V") ~1 ~~ ,I ;

+ de =:

369

-0.56486

coA +pyruvate + h20, 2, pH, . 2 5 ] ,

-0.475-

PH

-0.525. -0.55Show[{plotl, plot2, plotf, plot4, plots), Axesorigin-, {5, -.7}, PlotRange+ {-.7, O}]; E'O/V

-0.5.

-0.6: t

6

7

8

9 pH

9.4 Calculate the change in binding of hydrogen ions in the following 10 biochemical half reactions at 298.15 K, pHs 5 , 6, 7, 8, and 9 and ionic strengths of 0, 0.10, and 0.25 M. Plot the change in binding at ionic strength 0.25 M versus pH. C 0 2tot + 2e-= formate + H20 C 0 2tot + acetyl-CoA + 2 e - = pyruvate + CoA + H20 ketoglutarate + ammonia +2e- = glutamate + H20 pyruvate + ammonia +2e- = alanine + H20 pyruvate + C 0 2tot + 2e-= malate + H20 cystine + 2e-= 2 cysteine + H2 citrate + CoA + 2 e - = malate +acteyl-CoA + H20 O2(8) + 4e- = 2 H20 NAD,,+ 2 e - = NADred (10) N2(g) + Se-= 2 ammonia + H2(g)

(BasicBiochemData2 has to be loaded)

370

Mathematica Solutions to Problems calcappredpot [ e ~ nu-, , pHlist-, islist-] := Module[{energy}, (*Calculates the standard apparent reduction potential of a half reaction at specified pHs and ionic strengths for a biochemical half reaction typed in the form nadox+de==nadred. The names of the reactants call the corresponding functions of pH and ionic strength. nu is the number of electrons involved. pHlist and islist can be lists.*) energy = Solve [eq, de] ; (-l*energy[[l, 1, 211 / (nu*96.485)) /. pH-tpHlist /. is+islist plot5 = Plot [Evaluate[- (2* 96.485 / (8.31451 * .29815 *Log [lo]) ) * D [calcappredpot[pyruvate + co2tot + de == malate + h20, 2, pH, -251, p H ] 1, {BH, 5, g}, P1otRange-t {o, 3}, Axesorigin-, (5, O), AxesLabel -> {8'pH11, "ANHtl}];

I

t

6

7

8

9 pH

This result is reasonable because the chemical reference reaction shows that 2 hydrogen ions are bound. This is affected in the neighborhood of pH 6.2 by the binding of a hydrogen ion by bicarbonate and malate. As pH 9 is approached, the dissociation of the hydrogen ion from bicarbonate begins to have an effect. plot8 = Plot[Evaluate[- (4*96.485/ (8.31451* .29815*Log[lO])) * D[calcappredpot [02g + de == 2 * h20, 4, pH, .25], pH] 1, {pH, 5, 9), PlotRange -> (0, 5). Axesorigin -> {5, 0), AxesLabel -> {"pH", lrANxrm}];

AN, A 7

3-

2. 1.

plot9 = Plot [Evaluate[- (2* 96.485 / (8-31451* .29815 * Log[lO] ) ) * D[calcappredpot[nadox+de=:nadred, 2, pH, .25], pH]], { p H , 5, 9}, PlotRange -> {0, 5}, Axesorigin -> {5, 0). AxesLabel -> {"pH", 'rANH1'}] ;

Redox Reactions

I

I 6

7

8

9 pH

Plotlo = Plot[Evaluate[- (8*96.485/ (8.31451* .ZSSlS*Log[lO])) * D [calcappredpot[n2g + de ::2 *ammonia + h2g, 8, pH, .25] , pH] 1, {pH, 5, 9}, PlotRange -> ( 0 , 11), Axesorigin -> {5, 0), AxesLabel -> {llpH1l,

8-

6-

4-

2I

I

6

7

8

9 pH

plot1 = Plot[Evaluate[-(2*96.485/ (8.31451* .29815*Log[lO])) * D[calcappredpot [co2tot + de == formate + h20, 2, pH, -251, pH] 1, { p H , 5, 9) I PlotRange -> {0, ll}, UesOrigin -> {5, 0), AxesLabel -> {"pH", "ANH"}];

8. 64-

2.

/ -

plot2 = Plot [Evaluate[ - (2* 96.485 / (8-31451* -29815R Log [lo]) ) * D[calcappredpot [acetylcoA + co2tot + de :I pyruvate + COA + h20, 2, pH, .25], pH] 1, {pH, 5, 9). PlotRange -> {0, ll}, Axesorigin-> {5, 0}, AxesLabel -> {"pH", "ANH"}];

371

372

Mathernatica Solutions to Problems

ANH

10 8

6 4

2 6

7

8

9 pH

plot3

Plot [Evaluate[ - (2* 96.485 / (8.31451 * .29815 * Log [ 101 ) ) * D[calcappredpot [oxoglutarats2+ ammonia + de == glutamate + h20, 2, p H , -251, pH] 1 , { p H , 5, 9), PlotRange -> {0, 11). Axesorigin -> {5, 0}, AxesLabel -> { l l p H r r , llAN,lt}];

ANH

"_ 6

I

6

7

8

9- PH

plot4 = Plot[Evaluate[-(2*96.485/ (8.31451* .29815*Log[lO])) * D[calcappredpot[pyruvate+ammonia+de =alanine+h20, 2, p H , .25], pH]], ( p H , 5, 9}, PlotRange -> {O, ll}, Axesorigin -> (5, 0}, AxesLabel -> { " p H " , "AN,"}];

6

7

8

9- PH

plot6 = Plot [Evaluate[ - (2* 96.485 / (8.31451 * .29815 * Log [ 101 ) ) * D [calcagpredpot [cystineL+ de :Z 2 * cysteineL + h20, 2, p H , .25], p H ] 1, {BH, 5, 9) PlotRange -> ( 0 , 11}, Axesorigin -> {5, o), AxesLabel -> { " p H " , "AN,"}];

I

Redox Reactions

I

1086-

I

6

7

8

9 PH

plot7 = Plot [Evaluate[- (2* 96.485 / (8.31451 * .29815 *Log [lo]) ) x D [Calcappredpot[citrate + COA + de ::malate + acetylcoA + h20, 2, g H , . 2 5 ] , pH] ] , {pH, 5, 91, PlotRange-> {0, 11}, Axesorigin-> (5, 0), AxesLabel -> { r a g H g a ,8 1 A N H s ] ] ;

10-

86.

I

6

7

8

9 pH

Show[{plotS, plot6, glot7, plot9, plotlo}, PlotRange+ { O , ll), AspectRatio-, 1-51;

373

374

Mathematica Solutions to Problems

i

6-

I

6

7

8

9

PH

starting at top 10 6

7 5 9 9.5 Plot the change in binding of hydrogen ions versus pH at ionic strength 0.25 M for the following five biochemical reactions: (1) NAD,, + formate + H20 = "Ired + C 0 2tot ( 2 ) NAD,, + malate + H20 = NADred + C 0 2tot + pyruvate (3) NAD,, + ethanol = NADred + acetaldehyde (4) NAD,, + alanine + H20 = NADred + pyruvate + ammonia (5) NAD,, + malate + acetylcoA + H2 0 = NADred + citrate + coA (BasicBiochemData2 has to be loaded)

375

Redox Reactions

I n [ l Z l : = calctrGerx[ec, pHlist-, islist-] :=

Module[{energy}. (*Calculates the standard transformed Gibbs energy of reaction in kJ mol*-1 at specified pHs and ionic strengths for a biochemical reaction typed in the form atp+h2o+de=adp+pi. The names of reactants call the appropriate functions of pH and ionic strength. pHlist and is list can be lists.*) energy = Solve [eq, de] ; energyul, 1, 21 /. pH + pHlist /. is + islist]

I n [ l 3 / : = glotl=Plot [Evaluate[(1/(8.31451*.29815*Log[lO] ) ) *D[calctrGerx[nadox+ethanol+de==nadred

+acetaldehyde,gH,.25],gH]],{pH,5,9~,AxesOrigin->{5,O},\!\(AxesLabel \*'I\ " \ < \ !\ (AN\-H\) \ > \ U " 1 \ ) I ;

6

7

8

-> {"\",

9 pH

-1.5-2I n [ 1 4 ] : = ~lot2=Plot[Evaluate[(l/(8.3l45l*.298l5*Log[lO]))*D[calctrGerx[nadox+~alate+acetylcoA+

h2o+de::nadred+citrate+coA,pH,.25],pH]],{pH,5,9},~esOrigin-~{5,O},\!\~~esLabel 1\ ) ,PlotRange- > { 0, 2.5 1 1 ; { \ I1, \ * \ \ < \ !\ ( AN\-H\ ) \ >\

-

AN,

6

7

8

->

9 pH

-0.51

-2.5' I n [ 1 5 ] : =plot3=Plot [Evaluate[(1/(8.31451*.29815*Log[lO] ) ) *D[calctrGerx[nadox+alanine+h2o+de==na

dred+pyruvate+ammonia,gH,.25],gH]].{gH,5,9~,AxesOrigin->(5,O~,\!\(AxesLabel { \ la, \ * \ \ < \ !\ (AN\-H\) \ > \ '*I*1 \ ) ,PlotRange- > { 0, -2.5 1 1 ;

->

376

Mathematica Solutions to Problems

AN, 6

7

8

9 pH

-1.51

-2-

I n [ l 6 / : = plot4=Plot

[Evaluate[(1/(8.31451*.29815*Log[lO] ) ) *D[calctrGerx[nadox+fomate+h2o+de==na dred+co2tot,gH,.251,gH~~,(gH,5,9?,AxesOrigin-~~5,O},\!\~AxesLabel- > I"\", \ * If\ \ < \ !\ ( AN\-H\ ) \ >\ ''1' } \ ) ,PlotRange- > { 0, -2.5 1 ; 11

-21

-2.5 1n[17]:=

plot5-Plot [Evaluate[(1/(8.31451*.29815*Log[lO] ) ) *D[calctrGerx[nadox+malate+h2o+de~=nad red+gyruvate+co2tot,pHI.25],gH]],{~H,5,9~,AxesOrigin-~C5,-2.5~,\!\~AxesLabel -> { '' \ I' , \ * I' \ It\ < \ !\ (AN\-H\) \ >\ " " } \ ) ,PlotRange- > { 0, -2.5 1 ;

-0-5- -1 -1.5-

-2: I 6

7

8

9 pH

Redox Reactions

C

-0.5

-1

-1.5

-2

\\

-

6

7

8

9 pH

377

Chapter 11 Use of Semigrand Partition Functions 11.1 (a) Write out the semigrand partition function r ' for a system containing a weak acid and its basic form at a specified pH. (b) Write out the equation for A, G'" of acetate at zero ionic strength. (c) Evaluate this function for afG o at pH 5 and zero ionic strength. Use calcdGmat to confirm this value. (d) Calculate the semigrand partition function ' and use it to calculate A, G o of acetate at pH 5 . 11.2 (a) Calculate the further transformed Gibbs energies of formation of G6P, F6P, and F16BP at pH 7, I = 0, [ATP] = ~ W ~ and M ,[ADPI = 1G-'M at 298.15 K. (b) Calculate the further transformed Gibbs energy of formation of the pseudoisomer group. (c) Calculate the equi1ib;ium mole fractions for G6P, F6P, and F16BP. (d) Repeat this calculation at [ATPI = 1 0 - 2 M ,and [ADP] = 10-'M at 298.15 K.

11.3 (a) Print out the equation for the standard transformed Gibbs energy of formation of the pseudoisomer group consisting of G6P, F6P, and F16BP symbolically. Assume that the system contains one mole of the pseudoisomer group. (b) Print out the equation for the corresponding semigrand partition function r = exp[-GIRT]. (c) Calculate the amount of ATP bound by the pseudoisomer group at [ATPJ = 0.0001 M and [ADP] = 0.01 M and then at [ATP] = 0.01 M and [ADP] = 0.01 M. (d) Make the same calculation for the binding of ADP.

379

380

Mathematica Solutions to Problems

11.1 (a) Write out the semigrand partition function I- ' for a system containing a weak acid and its basic form at a specified pH. (b) Write out the equation for a, G o of acetate at zero ionic strength. (c) Evaluate this function for a, G o at pH 5 and zero ionic strength. Use calcdGmat to confirm this value. (d) Calculate the semigrand partition function r ' and use it to calculate A f G o of acetate at pH 5 .

(a) The standard transformed Gibbs energy for one mole of the pseudoisomer group at zero ionic strength is given by

-(In10 NH1 p H ) - pl/(r t ) -(In10 NH2 p H ) - p2/(r t) -(r t Log[E + E I)

The lnlO has been put in in this way so that the partition function would print in a simple way.

r' E

=Expr-(i/ (r*t))* g - ]

-(ln10 NH1 p H )

-

pl/(r t)

-(ln10 NH2 p H ) - p 2 / ( r t) + E

This is the semigrand partition function for the system. It was calculated from &GIo, but it could have been written down directly. (b) Write the equation for a, G'" of acetate at a specified pH. For the anion -369.31+3*r*t*Log[101 *pH

-369.31 + 3 p H r t Log[lOl

For the acid -396.45+4*r*t*Log[lOI *gH

-396.45 + 4 p H r t Log[lOl

The standard transformed Gibbs energy of the pseudoisomer group is given by

-((-369.31 + 3 p H r t ~og[lOl)/(rt)) -(r t Log[E -((-396.45 + 4 p H r t Log[lO])/(r t)) E I) gacetate/.r->S.31451/.t->.29815/.pH->5

-284.805

This value can be confirmed by use of calcdGmat. calcdQnat[acetatespl/.pH->5/.is->O

-284.805

,

Use of Semigrand Partition Functions

381

(d) Use r ' to calculate A, G o at pH 5. The partition function that is evident in the calculation of gacetate can be printed in traditional form.

Q

- 3 pH r t log(10)-369.31 rf

+ e-

4 pH r f log(10)-396.45 rl

The numerical value of the partition function for acetate at pH 5 is given by

7.85988 1 0

Since G ' =-RTlnr

49

I,

-8.31451*.29815*Log[E~[-(-369.31+3*r*t*Log[101pH~/~r*t~1+Exp~(-396.45+4*r*t*Log[lO]~H)/(r*t)ll/.r->8.31451/.t->.29815/.pH->5 -284.805

Thus the semigrand partition function contains all the information on the thermodynamics of the system containing acetate at a specified pH.

11.2 (a) Calculate the further transformed Gibbs energies of formation of G6P, F6P, and F16BP at pH 7, I = 0, [ATP] = 10-4M, and [ADP] = 1 0 - 2 M at 298.15 K. (b) Calculate the further transformed Gibbs energy of formation of the pseudoisomer group. (c) Calculate the equilibrium mole fractions for G6P, F6P, and F16BP. (d) Repeat this calculation at [ATP] = 1 0 - 2 M ,and [ADP] = 1 0 - 2 M at 298.15 K. (BasicBiochemData2 has to be loaded) (a) Calculate the standard transformed Gibbs energies of formation of the reactants at pH 7 and zero ionic strength gpatp=atp/.pH->7/.is->O

-2292.61 gpadp=adp/.pH->7/.is->O -1428.93

gpglucose6phos=glucose6phos/.pH-~7/.is->O -1325.

-1321.71

gpfructosel6phos=fructosel6phos/.pH-~7/.is-~O -2202.84

382

Mathematica Solutions to Problems

Now calculate the further transformed Gibbs energies of formation of these reactants at the specified concentrations of ATP and ADP gppglucose6phos=gpglucose6phos(~pat~+8.31451*.29815*Log[.0001~)+(~adp+8.31451*.29815*Log~.011~

-449.906 gppfructose6phos=ggfructose6~hos(~atg+8.31451*.29815*Log[.0001])+(~adg+8.31451*.29815*Log~.~11~ -446.611 gpgfructose16phos=ggfructosel6ghose16phos-2*(g~at~+8.31451*.29815*Log[.00011)+2*~gpadp+8.31451 *.29815*Log[.O11)

-452.647

(b) Calculate the further transformed Gibbs energy of formation of the speudoisomer group calciso CtransG-l := Module[{},(*This program produces the function of pH and ionic strength that gives the standard transformed Gibbs energy of formation of a pseudoisomer group at 298.15 K. The input is a list of the names of the functions for the pseudoisomers in the groups. Energies are expressed in kJ molA-l.*) -8.31451*.29815* Log[Apply[Plus, ExpC-1*transG/(8.31451*.29815)11]1

gppiso=calc~so[~ggpglucose6phos,gpgfructctosel6phoS~~

-453.514

(c) Calculate the equilibrium mole fractions r~=Exp[(g~~iso-{ggpg1ucose6phos,gppf~ctose6pho6,gppf~cto6e16phos})/(8.31451*.29815~1 { O .233262, 0.061748, 0.704991

(d) Now increase the ATP steady state concentration by a factor of 100 gppglucose6phos=gpglucose6phos(gpat~+8.31451*.29815*Log[.01l)+(ggadg+8.31451*.29815*Log~.011~

-461.322 gppfructose6phos=gpfructose6phos(ggatp+8.31451*.29815*Log[.Oll)+(gpadg+8.31451*.29815*Log[.Ol~ -458.027

gppfructose16phos=gpf~ctose16phos-2*(ggatp+8.31451*.29815*Log1.011~+2*~~~ad~+8.31~~1*. 29815*Log I.011 1

-475.48

-475.49

Use of Semigrand Partition Functions

383

ri=Exp[(g~piso-{gppg1ucose6~hos,~pfructose6phos,gppfru~tose16phos})/~8.31451*.29815~1 I0.00329493,

0.00087222,

0.995833)

A higher concentration of ATP causes more F16BP to exist at equilibrium. 11.3 (a) Print out the equation for the standard further transformed Gibbs energy of formation of the pseudoisomer group consisting of G6P, F6P, and F16BP symbolically. Assume that the system contains one mole of the pseudoisomer group. (b) Print out the equation for the corresponding semigrand partition function r ' ' = exp[-G ' ' /RT]. (c) Calculate the amount of ATP bound by the pseudoisomer group at [ATPI = 0.0001 M and [ADP] = 0.01 M and then at [ATP] = 0.01 M and [ADP] = 0.01 M. (d) Make the same calculation for the binding of ADP.

This should be run when Problem 11.2 is still in the workspace. (a) Print out the equation for the standard further transformed Gibbs energy of formation of the C 6 pseudoisomer group -8.31451*.29815*Log[Exp[-(gpglucose6phos(gpatp+8.31451*.29815*Log[ATP])+(g~adp+8.31451*.29815*Log~~Pl~~/(8.31451*.29815~1+Exp~ (gpfructose6phos(gpatp+8.31451*.29815*Log[ATP])+(gpadp+8.31451*.29815*Log[ADPl))/(8.31451*.29815~1+Exp~

-

(gpfructose16phos-2*(~atp+8.31451*.29815*Log~ATP1)+2*(gpadp+8.31451*.29815*Log~~P1~~/ (8.31451*.29815)11

-2.47897 Log[E E

-0.403393

-0.403393

( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 Log[ADPI

-

2 . 4 7 8 9 7 LOg[ATPI)

( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATPI)

Power[E, -0.403393

+

+

( - 2 2 0 2 . 8 4 + 2 ( - 1 4 2 8 . 9 3 + 2.47897 Log[ADPI) -

2 (-2292.61 + 2.47897 Log[ATPI))II

-2.47897 10g(e-0.403393

(2.47897 log(ADP)-2.47897 log(ATP)-461.322)

e-0.403393 (2.47897log(ADP)-2.47897 10g(ATP)-458.027)

+

+

e-0.403393 (2 (2.47897log(ADP)-1428.93)-2 (2.47897log(ATP)-2292.61)-2202.84)1 Note that the species concentrations of ATP and ADP are in the exponents (b) Print out the semigrand partition function gamma=Exp[Log [ExpC- (gpglucose6phos(gpatp+8.31451*.29815*Log[ATPl)+(g~adp+8.31451*.29815*Log[~P]))/(8.31451*.29815)]+Ex~~ -(gpfructose6phos(gpatp+8.31451*.29815*Log[ATPl~+(g~adp+8.31451*.29815*Log[ADP]))/(8.31451*.29815)1+Expt

-

(gpfructose16phos-2*(~atp+~.31451*.29815*Log[ATP])+2*(gpadp+8.31451*.29815*Log[ADP]~~/ (8.31451*.29815)111

384

Mathematica Solutions to Problem -0.403393

E

E

( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 LoglADP] - 2 . 4 7 8 9 7 L o g [ A T P ] )

-0.403393

+

( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATPI) t

Power[E, -0.403393 ( - 2 2 0 2 . 8 4 + 2 ( - 1 4 2 8 . 9 3 + 2 . 4 7 8 9 7 Log[ADPI) 2 (-2292.61 + 2.47897 Log[ATPI))I

TraditionalForm[gal

e-0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-46 1.322) b?

+

-0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-4.58.027)

+

a? -0.403393 (2 (2.47897 log(ADP)- 1428.93)-2 (2.47897 log(ATP)-2292.61)-2202.84) Note that the first Exp and Log in gamma cancel so that the same result is obtained with

(gpfructosel6phos-2*(ggatp+8.31451*.29815*Log[ATP])+2* (gpadp+8.31451* .29815*Log[ADPl) / (8.31451*.29815)1 E

( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 LoglADP] - 2 . 4 7 8 9 7 LOg[ATPI)

-0.403393 E

-0.403393

Power[E,

( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATPI)

-0.403393

( - 2 2 0 2 . 8 4 + 2 ( - 1 4 2 8 . 9 3 + 2 . 4 7 8 9 7 LogLADPI) -

2 ( - 2 2 9 2 . 6 1 + 2 . 4 7 8 9 7 Log [ATPI ) ) 1

TraditionalForm [gamma21

e -0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-461.322) b?

+

-0.403393 (2.47897 10g(ADP)-2.47897 log(ATP)-458.027)

+

-0.403393 (2 (2.47897 log(ADP)- 1428.93)-2 (2.47897 Iog(ATP)-2292.61)-2202.84)

&?

(c) The fundamental equation for G" shows that the amount of ATP bound by the pseudoisomer group is given by nc(ATP) = 2lnF/2ln[ATP] at constant [ADP]. There is a corresponding equation for ADP. boundATP=D [Log[gamma2],Log [ATPII

1.

(

E

0 . 4 0 3 3 9 3 ( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATP])

+

1.

E

0 . 4 0 3 3 9 3 ( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADPl

2 . / PowerrE,

-

2.47897 LoglATP])

'

0 . 4 0 3 3 9 3 (-2202.84 + 2 ( - 1 4 2 8 . 9 3 + 2 . 4 7 8 9 7 Log[ADPI) -

2 (-2292.61 + 2.47897 Log[ATPI))I) / - 0 . 4 0 3 3 9 3 ( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 LOglADPI - 2 . 4 7 8 9 7 LOg[ATPI) (E - 0 . 4 0 3 3 9 3 ( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATPI)

E

' +

PowerLE, - 0 . 4 0 3 3 9 3 ( - 2 2 0 2 . 8 4 + 2 ( - 1 4 2 8 . 9 3 + 2 . 4 7 8 9 7 L o g [ A D P ] ) 2 (-2292.61 + 2.47897 Log[ATP]))I)

-

Use of Semigrand Partition Functions

385

Tradi tionalFormtboundATP1

(1. a?-0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-461.322)

+

1. a?- 0.403393 (2.47897log(ADP)-2.47897 log(ATP)-458.027)

2. a?-0.403393 (2 (2.47897log(ADP)-I428.93)-2

+

(2.47897log(ATP)-2292.61)-2202.84)

)/

(a?-0.403393 (2.47897 log(ADP)-2.47897 10g(ATP)-461.322) + a?

-0.403393 (2.47897log(ADP)-2.47897 Iog(ATP)-458.027)

+

(2 (2.47897log(ADP)-I428.93)-2 (2.47897log(ATP)-2292.61)-2202.84)

.-0.403393

1

boundATP/.ATP->.QOQl/.ADP->.Ol 1.70499

boundATP/.ATP->.Ql/.ADP->.QI 1.99583

As the concentration of ATP is increased, F16BP will predominate more and more and this average number bound will approach 2 .

boundADP=D[Log[ganrma2 1 ,Log [ADPI1 -1. ( 0.403393

E

(-461.322

+ 2 . 4 7 8 9 7 Log[ADP]

-

2.47897 Log[ATP]) -

( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 LOg[ADP] - 2 . 4 7 8 9 7 L o g [ A T P ] )

0.403393

E

2 . / Power[E, 0.403393 (-2202.84 + 2 (-1428.93

+ 2 . 4 7 8 9 7 Log[ADPI) -

2 (-2292.61 + 2.47897 LOg[ATP]))I) / (E

( - 4 6 1 . 3 2 2 + 2 . 4 7 8 9 7 LOg[ADP] - 2 . 4 7 8 9 7 LOg[ATP])

-0.403393

E

-0.403393

Power[E,

( - 4 5 8 . 0 2 7 + 2 . 4 7 8 9 7 Log[ADP] - 2 . 4 7 8 9 7 LOg[ATP])

-0.403393

+ +

(-2202.84 + 2 (-1428.93 + 2.47897 Log[ADPI)

-

2 (-2292.61 + 2.47897 LOg[ATPI))I)

TraditionalFormtboundADPl

(- 1. a?-0.403393 (2.47897 10g(ADP)-2.47897 log(ATP)-461.322) 1. a?-0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-458.027) -

2. a?-0.403393 (2 (2.47897 log(ADP)-1428.93)-2

(2.47897log(ATP)-2292.61)-2202.84)

0.403393 (2.47897 log(ADP)-2.47897 Iog(ATP)-461.322)

(6-

Q?

>/

+

-0.403393 (2.47897 log(ADP)-2.47897 log(ATP)-458.027)

+

a?-0.403393 (2 (2.47897log(ADP)- 1428.93)-2 (2.47897 Iog(ATP)-2292.61)-2202.84)

boundADP/.ATP->.QQQl/.ADP->.Ql -1.70499

386

Mathematica Solutions to Problems boundADP/.ATP->.01/.ADP->.01 -1.99583

As the concentration of ATP is increased, F16BP will predominate more and more and this average number bound will approach -2. Note the binding of ADP is the same as the binding of ATP except for sign.

Index of Mathematica Programs (Problem numbers are given, and Pkg indicates that the program is in the package BasicBiochemData2.) calcappredpot[eg_, nu-, pHlist-, islist-], Pkg, 9.1, 9.3, 9.4 calcdG3I [reactantname-], Pkg calcdG5pH [reactantname-] , Pkg calcdGHT[speciesmat-1, Pkg, 4.6, 8.1 calcdGis[sp-l, 3.1, 3.3 calcdGmat [speciesmat-1 , Pkg, 4.1 calCdGTsp [speciesmat-, temp-, ionstr-I, 3.6 calcdH3I[reactaanth-], Pkg calcdH5pHtreactanth-I, Pkg calcdHinat [speciesmat-1 , Pkg, 4.2 calcdHTgg tspeciesmat-I

, 4.2

calcdHTsp [speciesmat-, temp-, ionstr-1

, 3.8

calcGeflsg[eguat-,pH_,ionstr-,zl-,nHl-],

Pkg

c a ~ c G e f 2 s p [ e g u a t ~ , p H _ , i o n s t r _ , z l ~ , n H l ~ , p K O Pkg ~l, c a ~ c G e f ~ s p [ e q u a t ~ , p H _ , i o n s t r ~ , z l ~ , n H l ~ , p K l O ~ , p KPkg 201,

calcgfDKtke~,conco2~],7.2 calcgfTf[keg_,conco2~], 7.1 calciso ItransG-I, 11.2 calckprimetec, pHlist-,islist-l, calckrx[ec, islist-], 3.1,

Pkg, 4.3, 4.4, 4.5, 4.9,

4.10, 6.4, 6.5, 9.2

6.4

c a l c N H r x ~ e ~ , p H l i s t ~ , i s l i s t ~Pkg, l , 4.8 calcpK[speciesmat-, no-,is-l, calcrow[ee, pHlist-,

islist-,

Pkg, 1.10, 1.11 rx-I

, 4.7

calcrxthermotabteg_,pHlist-,islist-],

Pkg

calctgfDlkeC, conco2-I, 7.2 calctgfT[keg_, conco2-I, 7.1 calctrGerxCee, pHlist-,

islist-], Pkg, 4.3, 4.6, 4.9, 4.10, 8.2, 9.5

calctrGerxTlee, pHlist-, islist-, tlist-I, 8.1, 8.2 equcalcc [as-.

Ink-, no-] ,Pkg, 6.6, 6 -7, 6.8

387

388

Index of' Mathernatica Programs epucalcrx[nu-, lnkr-, mkeqm[c-List,

no-] ,Pkg,

6.4,

6.6, 6.7, 6.8

s-List], Pkg, 6.1, 6.2, 6.3

nameMatrix[m-List, s-List] , Pkg, 6.1, 6.2, 6.3 round[vec-, params-: (4, 211, 4.7

rxthermotab[e~,gHlist-,islist-l, 4.8

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty Copyright 0 2003 John Wiley & Sons, Inc. ISBN 0-471-22851-6

Index

Acid dissociation constants biochemical reactions at specified pH, species and reactants, transformed thermodynamic properties, 65-66 carbon dioxide equilibrium distribution, gas phase and aqueous solution. 151 152 complex ions, 3-5 diprotic acid, 132-133 half-reactions with multiple species at specified pH, 163-165 research background, 1-2 Activity coefficient aqueous systems, chemical equilibrium equilibrium constant derivation, 37-38 ionic strength, 46-47 complex ions, 3-5 Adair equation, hemoglobin tetramers, oxygen binding by, 123 --124 Adenosine diphosphate (ADP) ATP hydrolysis, hydrogen and magnesium ion production, 13--15 biochemical reactions apparent equilibrium constants, 11-13 composition calculations, 110-1 14 glycolysis considerations, 114- 1 17 nitrogenase reaction, 165-167 Adenosine triphosphate (ATP) binding of hydrogen and magnesium ions, 5- 11 biochemical reactions apparent equilibrium constants, 11- 13 composition calculations, 110- 114 glycolysis considerations, 114-1 17 hydrolysis of, hydrogen and magnesium ion production, 13--15 nitrogenase reaction, 165-167 Alcohol fermentation, Gibbs energy changes, 2 Apparent conservation matrix biochemical equations, 96-97 biochemical coupling reactions, 98-99 glycolysis reactions, 115-117 Apparent equilibrium constant biochemical reactions at specified pH, 63-65 ionic strength gluconeogenesis, 82, 84 -

transformed Gibbs energies, 74676 nitrogenase reaction, 167 protein binding of ligands, 129- 132 Apparent stoichiometric matrix, biochemical equations, 97 Aqueous systems chemical equilibrium equilibrium constant derivation, 36--38 Gibbs-Duhem equation, phase rule and, 43-44 ionic strength, solution reaction equilibria, 46-47 isomer group thermodynamics, 44-46 research background, 35--36 temperature effects on thermodynamics, 47--49 thermodynamic properties in chemical reactions, 38-43 thermodynamic tables, biochemical species, 49- 55 ionic strength, 3-5 phase equilibrium carbon dioxide equilibrium, gas phase/aqueous solution distribution, 150- 152 high polymers, 152-153 molar properties of ions, electric potentials, 148- 149 research background, 141- 142 two-phase systems chemical reaction, membrane permeability, single ion, 146-147 transformed Gibbs energy, 148 chemical reaction and semipermeable membrane. 144-145 membrane permeability, single ion, 145- 146 no chemical reaction, 142-143 weak acid pKs, 15-17 Average binding, ATP to hydrogen ions, 7 -1 1

B Binding capacity calorimetric measurements, transformed enthalpy of reaction from species formation, 173- 174 hydrogen ions, protein-ligand equilibria, pH lecels and, 137-138 Binding polynomials ATP binding of hydrogen and magnesium ions, 8- 11 transformed Gibbs energy, specified oxygen concentration, 127

390

Index

Binding potential, transformed Gibbs energy, specified oxygen concentration, 127 Biochemical reactions apparent equilibrium constants. 11- 13 aqueous systems, chemical equilibrium, thermodynamic tables, 49%55 calorimetry research background, 17 1 172 temperature effects. 176 177 transformed enthalpy determination reaction, 172 species formation, 172- 174 transformed entropy determination, 174 175 compositions calculations, thermodynamic Icvcls, 1 10 1 I4 equilibrium compositions calculations, 108- 110 glycolysis, calculations for, 117 1 19 glycolysis at specified reactants, 114- 117 matrix equations. 95-97 coupling reactions, 97 99 fundamental equations, 101 102 net reactions calculation, matrix multiplication, 106- 107 oxidation-reduction reactions, basic equations, 156- 158 pathways calculation. linear equations, 107 semigrand ensemble partition function. coenzyme concentrations, 183- 184 systems of. basic properties. 105 thermodynamics at specified pH apparent equilibrium constant, 63-65 fundamental equation, 58-62 Gibbs-Duhem equation, degrccs o f freedom, and equilibrium criterion, 70 71 Gibbs energy tansformations, apparent equilibrium constants. 74 76 hydrogen ion binding, 71 -~72 ionic strength, transforincd properties tables, 76 4 6 magnesium ion binding. 72 73 pseudoisomer groups, 68- 69 reaction plots. 86-8s speciesireactants, transformed properties, 65-66 temperature effects. 73~-74 transformed properties. 66 68 water reactants, Legendre transform for, 107- 108 Boltzniann constant, thermodynamic potentials, monatomic ideal gas, 33 -34 ~

C Callen nomenclature, Legendre transforms for thermodynnmic potentials. 30 Calorimetry, biochcmical rcactions research background. 17 1 I72 tcinpcrature effects, 176 177 transformed enthalpy determination reaction. 172 species formation, 172- I74 transformed entropy determination, 174 175 Canonical ensemble partition function, single species singlephase systems, thermodynamic potentials, 30-32 Canonical forms, chemical cquations as matrix equations, 92-95

Capacitance measurements, two-phase aqueous systems, single-ion membrane permeability, 145- 146 Carbon dioxide. equilibrium distribution, gas phase and aqueous solution, 150 152 Charge relaxation, two-phase aqueous systems. single-ion membrane permeability, 145 146 Chemical equilibrium, aqueous systems equilibrium constant derivation, 36-38 Gibbs-Duhem equation, phase rule and. 43 --44 ionic strength, solution reaction equilibria, 46-45 isomer group thermodynamics, 44- 46 research background, 35536 temperature effects on thermodynamics, 47-49 thermodynamic propertics in chemical reactions, 38 43 thermodynamic tables, biochemical species. 49 55 Chemical potential aqueous systems chemical equilibrium, isomer group thermodynamics. 44 46 phase equilibrium, two-phase systems, single-ion membrane permeability, 146 biochemical reactions at specified pH, transformed potentials, 59-62 internal energy equation, 22 24 transformed Gibbs energy, specified oxygcn concentration. I25 I27 two-phase aqueous systems. transformed Gibbs energy, I48 Chemical reactions aqueous systems. two-phase systems semipermeable membrane, 144- 145 single-ion membrane permeability. 146&147 chemical equations as matrix equations, 90 95 fundamental equations, matrix form. 99 101 Citric acid cycle biochemical reactions at specified pH apparent equilibrium constants, 82, 85 transformed Gibbs energies, 82. 84 Gibbs energy changes, 2 Clapeyron equation, aqueous systems, phase equilibrium. single species two-phasc systcms, 142 143 Coenzyme concentrations, semigrand cnsemblc partition function, 183- 184 Complex ions. acid dissociation and dissociation constants. 3-5 Components aqueous systems, chemical equilibrium, 42--43 biochemical equations as matrix equations, 97 chemical equations as matrix equations. 90 95 fundamental equations, matrix form, 100-~ 101 Conjugate pairs extensivehtensive properties, 32 internal energies, 23-24 Conservation matrices biochemical equations as matrix equations, 95-97 chemical/biochemical thermodynamics, 89-90 chemical equations as matrix equations. 90 95 chemical reactions, 90-95 glycolysis reactions, specific rcactants. 1 I5 117 water reactants, Legendre transform calculations. 107-108 Cooperative effect, protein-ligand equilibria. pH levels, 135-138 ~

~

~

Index Counterions, two-phase aqueous systems, single-ion membrane permeability, 145- 146 Coupling reactions, matrix equations, biochemical reactions, 97-99

D

deb ye-Huckel equation aqueous systems, chemical equilibrium ionic strength, 46-47 temperature effects, 47-49 biochemical reactions at specified pH, temperature effects, 73-74 ionic strength, 4 Debye length, two-phase aqueous systems, single-ion membrane permeability, 145 - 146 Degrees of freedom aqueous systems, chemical equilibrium, Gibbs-Duhem equation, phase rule, 43- 44 biochemical reactions at specified pH, 70-71 phase rule, Gibbs-Duhem equation, 25 --26 Dependent variables, biochemical reactions at specified pH, 59-62 Deriatives, thermodynamic potentials, monatomic ideal gas, 32-34 Dimers, tetramer partial dissociation into, 127-129 Diprotic acid, dissociation constants, 132.- 133 Dissociation constants. See also Acid dissociation constants complex ions, 3-5 diprotic acid, 132-133 protein-ligand equilibria, pH levels and, 134- 138 Double species two-phase systems, aqueous systems, chemical equilibrium, 143

E Equcalcrx, equilibrium calculations, biochemical reaction systems, 109-110 Electric potential, aqueous systems. phase equilibrium molar properties of ions, 148-149 single-ion membrane permeability, chemical reaction, 147 Enthalpy aqueous systems chemical equilibrium, 41 -43 ionic strength, 47 temperature effects, 48--49 phase equilibrium, electrical potentials, effects on ion molar properties, 149 biochemical reactions at specified pH, 60-62 apparent equilibrium constant derivation, 64-65 pseudoisomer thermodynamics, 68-69 thermodynamic properties’ plots, 86-88 transformed enthalpy of reaaction, 67 -68 calorimetric measurements research background, 171 172 transformed enthalpy biochemical reaction, 172 species formation, 172-174 Legendre transforms for thermodynamic potentials, 26-30 -

391

Enthalpy of dissociation, calorimetric measurements, 172 Entropy aqueous systems chemical equilibrium, 41 -43 isomer group thermodynamics, 45-46 temperature effects, 48-49 phase equilibrium, electrical potentials, effects on ion molar properties, 149 biochemical reactions at specified pH, 60 -62 calorimetry, transformed entropy of biochemical reactions, 174- 175 fundamental equation for, 21-24 molar entropy, Legendre transforms for thermodynamic potentials, 28-30 second law of thermodynamics, 19 Enzyme catalysis biochemical thermodynamics, 2 composition calculations, 110-1 14 Legendre transform, 113-1 14 matrix equations, biochemical reactions, coupling reactions, 97-99 oxidation-reduction reactions methane monooxygenase reaction, 162-163 single species at specified pH, 162 transformed Gibbs energy. fumarase catalysis, 138- 139 Equations of state, internal energies, 23 Equcalcc program, equilibrium calculations, biochemical reaction systems, 109- 110 Equilibrium condition aqueous systems, chemical equilibrium constant derivation. 36--38 biochemical reactions at specified pH apparent equilibrium constant derivation, 64-65 calculations for, 108-1 10 Gibbs-Duhem equation, 70-71 glycolysis, 117-- 119 chemical equations, matrices, 90-95 Equilibrium constants acid dissociation constants, 3-5 aqueous systems, chemical equilibrium, 36-38 biochemical reactions, 11 13 biochemical thermodynamics, 2-3 carbon dioxide equilibrium distribution, gas phase and aqueous solution, 151-152 complex ion dissociation constants, 3 -5 hemoglobin tetramers, oxygen binding by, 123- 124 hydrogenlmagnesium ions adenosine triphosphate (ATP) binding, 5- 11 adenosine triphosphate (ATP) hydrolysis, 13-15 protein binding of ligands experimental determination, 129-132 p H levels and, 134-138 research background, 1--2 tetramers, partial dissociation into dimers, 127-129 weak acid pKs, 15-17 Euler’s theorem, internal energy equation, 24 Exact function, Maxwell equation, 25 Extensive thermodynamic properties chemical potential, 23 defined, 21 Extent of reaction, aqueous systems, chemical equilibrium constant derivation, 36-38 ~

392

Index

F First law of thermodynamics, internal energy, 19-24 Fractional saturation apparent equilibrium constant determination, 129- 132 dimers, partial dissociation of tetramers into, 128- 129 hemoglobin tetramers, oxygen binding by, 123- 124 Fumarase catalytic sites, transformed Gibbs energy, 138- 139 protein-ligand equilibria, pH levels, 135 - 138 Fundamental equations of thermodynamics aqueous systems, phase equilibrium, 141b 142 double species two-phase systems, 143 electrical potentials, effects 011 ion molar properties. 1 4 8 ~149 N,species, two phases, 143 single species two-phase systems, 142- 143 two-phase chemical reaction. semipermeable membrane, 144~-145 two-phase systems, single-ion membrane permeability, 145-146 biochemical reactions matrix equations, 101-102 specified pH, 58-62 chemical reactions, matrix equations, 99- 101 hemoglobin tetramers, oxygen binding by, 122&124 internal energy, 21-24 matrices for, 90 biochemical reaction systems, 101- 102 chemical equations, 99-101 principles of, 19- 20

G Gaseous reactions carbon dioxide equilibrium distribution, gas phase and aqueous solution, 150-- 152 chemical equations as matrix equations, 91 -95 Gaussian reduction, linear algebra, 103 Gibbs-Duhem equations aqueous systems chemical equilibrium phase rule, 43-44 single-ion membrane permeability, chemical reaction, 147 phase equilibrium, 141 142 double species two-phase systems, 143 N, species, two phases, 143 single spccies two-phase systems, 142-143 two-phase chemical reaction, semipermeable membrane. 144-145 two-phase systems, single-ion membrane permeability, 146 biochemical reactions at specified pH, 70 71 composition calculations, Legendre transform, 112-114 matrices, 90 fundamental biochemical equations, 101--lo2 fundamental chemical equations. 101 phase rule and, 25 26 Gibbs energies. See i d s o Transformed Gibbs energy aqueous systems

chemical equilibrium energy of formation, 39-43 ionic strength, 47 isomer group thermodynamics, 44-46, 45%46 reaction Gibbs energy, 36-38 thermodynamic tables, biochemical species, 49-55 phase equilibrium single-ion membrane permeability, 146 148 two-phase chemical reaction, semipermeable membrane, 144--145 biochemical reactions at specified pH apparent equilibrium constant derivation, 64 65, 74 76 pseudoisomer thermodynamics, 68-69 species and reactants, transformed thermodynamic properties, 65-66 transformed Gibbs, 58-62 biochemical thermodynamics, 2 3 chemical reactions, fundamental equations, matrix form. 99 101 equilibrium compositions, biochemical reaction systcms, 108-110 internal energy equation, 22-24 Legendre transforms, 20 for thermodynamic potentials, 26--30 oxidation-reduction reactions, 155- 156 semigrand ensemble partition function, 180 181 thermodynamic potentials Legendre transforms, 26 - ~ 3 0 monatomic ideal gas, 33- 34 water reactants, Legendre transform calculations, 107 108 Gibbs-Helmholtz equation aqueous systems, chemical equilibrium, 41 -43 ionic strength, 47 biochemical reactions at specified pH, 62 apparent equilibrium constant derivation, 65 pseudoisomer thermodynamics, 69 calorimetry of biochemical reactions, temperature effects, 176&177 Legendre transforms for thermodynamic potentials, 28- 30 Gluconeogenesis, biochemical reactions at specified pH, transformed reaction Gibbs energies, 82-83 Glycolysis biochcmical reactions at specified pH composition calculations, Legendre transform, 113 I14 equilibrium conditions, 117- 119 specified reactant calculations, 114-1 17 transformed reaction Gibbs energies, 81 -82 Gibbs energy changes, 2 net reaction calculation, matrix multiplication, 106 - I07 semigrand ensemble partition function, coenzyme concentrations, 184 Grand canonical ensemble partition function semigrand ensemble partition function and, 180- 18I single species single-phase systems, thermodynamic potentials, 31 -32 ~

~

H Half-reactions basic equations, 157-158 hydrogen ion binding at specified pH, 167- 170

Index multiple species reactants at specified pH, 163-165 nitrogenase reaction, 165- 167 research background, 155- 156 single species at specified pH, 158-162 Hamiltonian equation, Legendre transforms for thermodynamic potentials, 26-30 Heat capacity of reaction aqueous systems, chemical equilibrium, 41 -43 isomer group thermodynamics, 46 calorimetry. 171 172 temperature effects, 176 - 177 Helmholtz energy, Legendre transforms for thermodynamic potentials, 26-30 Hemoglobin tetramers fractional saturation, apparent equilibrium constant determination, 129-132 oxygen binding, 122-124 Henry’s law constants, carbon dioxide equilibrium distribution, gas phase and aqueous solution, 151152 High polymers, phase separation in aqueous systems with, 152- 153 Hydrogen ions adenosine triphosphate (ATP) binding, 5- 11 adenosine triphosphate (ATP) hydrolysis, 13- 15 binding of, half-reactions at specified pH, 1 6 7 ~170 biochemical reactions at specified pH binding calculations, 71 -72 gluconeogenesis, ionic strength, 82, 84 glycolysis, ionic strength, 82-83 pyruvate dehydrogenase, citric acid cycle, and net reaction, ionic strength, 82, 85 transformed thermodynamic properties, 65-66 caloritnetric measurements, transformed enthalpy of reaction from species formation, 173- 174 protein-ligand equilibria, pH lcvels and, 136- 138 Hydrolysis adenosine triphosphate (ATP), hydrogen and magnesium ion production, 13- 15 biochemical coupling reactions, matrix equations, 98-99 chemical equations as matrix equations, 94 95 Gibbs energy changes, 2 nitrogenase reaction, 165- 167 -

I Identity matrices, chemical equations as matrix equations, 92-95 Independent variable, biochemical reactions at specified pH, 59-62 Tnexact function, Maxwell equation, 25 Integrated fundamental equation, Legendre transforms for thermodynamic potentials, 28-30 Intensive thermodynamic properties chemical potential, 23 defined, 21 Internal energy first law of thermodynamics, 19-20 fundamental equation for, 21-24 Ionic strength aqueous systems, 3-5

393

chemical equilibrium, 46-47 constant derivation, 37- 38 molar properties, electric potential effects, 148- 149 thermodynamic tables, biochemical species, 49-55 biochemical reactions at specified pH binding calculations, 71 ~ - 7 2 gluconeogenesis, 82, 84 glycolysis, 82-83 half-reactions and hydrogen ion binding, 168- 170 pyruvate dehydrogenase, citric acid cycle, and net rcaction, 82, 85 thermodynamic properties’ plots, 86-88 transformed thermodynamic properties, 65-66 transformed thermodynamic properties at 298.15 K, tables of standards, 76-86 oxidation-reduction reactions basic equations, 157--158 methane monooxygenase reaction, 162- 163 single species at specified pH, 158-162 Isomer group thermodynamics, aqueous systems, chemical equilibrium, 44- 46 Isothermal-isobaric partition function semigrand ensemble partition function and, I80 - 181 single species single-phase systems, thcrmodynamic potentials, 31-32

L La Chatelier’s principle aqueous systems, chemical equilibrium, isomer group thermodynamics, 46 ATP hydrolysis, hydrogen and magnesium ion production, 15 Lagrangian functions equilibrium calculations, biochemical reaction systems, 109-110 Legendre transforms for thermodynamic potentials. 26-30 Laplace transforms, semigrand ensemble partition function, weak acid systems as specific pH, 182- 183 Legendre transforms biochemical reactions composition calculations, 1 1 1 - 1 14 specified pH, 58-62 apparent equilibrium constant derivation, 63-65 general principles, 105 Gibbs-Duhem equation, 70-71 magnesium ion binding calculations, 72-73 transformed Gibbs energy, apparent equilibrium constant derivation, 74-76 water reactants, 107T108 biochemical thermodynamics, Gibbs free energies, 3 conjugate pairs, extensive/intensive properties. 32 internal energy equation, 22-~24 matrix equations biochemical coupling reactions, 99 biochemical fundamental equations, 102 principles of, 20 thermodynamic potentials, 26-30 single species single-phase systems, 30-32 transformed Gibbs energy, specified oxygen concentration. 125-127

394

Index

Legendre transforms (Contiriiird) two-phase aqueous systems, transformcd Gibbs energy, 148 Ligands, protein binding of, thermodynamics diprotic acid dissociation, 1 3 2 133 ~~ cquilibrium constants, determination, 129- 132 oxygen binding, hemoglobin tetraniers, 122 124 pH levels, 134 138 research backgro tind, 1 2 1 1 22 tetramer-to-dimer partial dissociation, 127 -~129 transformed Gibbs encrgy fumarase catalysis, 138- 139 oxygcn concentrations, 125- 127 Limiting laws, ionic strength, 3-4 Linear algebra biochemical reactions, pathways calculation, 107 matrix equations, biochemical reaction systems, 103 Linked functions, ATP binding of hydrogen and magnesium ions. I 1 ~~

-

M

aqueous systems, phase equilibrium, electrical potentials, effects on ion molar properties. 149 biochemical reactions at specified pH, 60- 62 Molar entropy aqueous systems, phasc equilibrium, electrical potentials, effects on ion molar properties, 149 biochemical reactions at specified pH, 60 62 calorimetry, transformed entropy of biochemical reactions. 174-175 Legendre transforms for thermodynamic potentials. 28-30 Molar heat capacity systems, chemical equilibrium, 41-43 isomer group thermodynamics, 46 temperature effects, calorimetry of biochemical reactions. 176-177 Molar volume Legendre transforms for thermodynamic potentials, 2X-30 thermodynamic properties. 21 Mole fractions ATP binding of hydrogen and magnesium ions, 6 - 1 I calorimetric measurements, transforincd cnthalpy of reaction from species formation, 173 I74 transformcd Gibbs energy, specified oxygeii concentration, 126-127 Monatomic ideal gas, thermodynamic potential derivatives. 32- 34 Multiple species reactants, half-reactions at specified pH. 163-165 ~

Magnesium ions adenosine triphosphate (ATP) binding, 5- 1 1 adenosine triphosphate (ATP) hydrolysis, 13- 15 biochemical reactions at specified pH, binding calculations, 72-73 calorimetric measurements, transformed enthalpy of reaction from species formation. 173 -174 Matrix equations, thermodynamics biochemical matrix equations, 95-97 biochemical reaction coupling, 97F99 chemical matrix equations, 90-95 chemical reaction systems, fundamental equations. 99 - 101 fundamental equations, biological reaction systems, 101 102 h e a r algebra operations. 103 Matrix multiplication h e a r algebra, 103 net biochemical reactions. 106 107 Maxwell equations aquous systems, chemical equilibrium, Gibbs ene,rgy of formation, 40 43 ATP binding of hydrogen and magnesium ions, 11 biochemical reactions at specified pH apparent equilibrium constant derivation, 64- 65 hydrogen ions, binding calculations, 7 1 72 composition calculations, 112- I14 Legendre transforms for thermodynamic potentials, 30 single species single-phase systems, thermodynamic potentials, 31 32 thermodynamics, 24 25 Membrane permeability. See also Semipermeable membrane two-phase aqueous systems, single ion permeation chemical reaction, 146- 147 phase equilibrium, 145--146 transformed Gibbs energy, 148 Metal ion complcxes, dissociation constants, research background, 1-2 Methane monooxygenase reaction, oxidation-reduction reactions, 162 163 Molar enthalpy ~

N Natural variables biochemical reactions at specified pH Gibbs-Duhein equation. 70-71 transformed Gibbs energy, 58-62 internal energy equation, 24 Legendre transforms for thermodynamic potentials, 27--30 Nernst cquation, oxidation-reduction reactions, 157 Net biochemical reactions, matrix multiplication, 106- 107 Newton-Raphson algorithm. equilibrium calculations. biochemical rcaction systems, 10% 110 Nicotinamide adenine dinucleotide-oxidized (NADox). biochemical reactions, glycolysis considerations. 114-117 Nicotinamide adenine dinucleotide-reduccd (NADred), biochemical reactions, glycolysis considerationa. 114-117 Nitrogcnase reaction, oxidation-reduction reactions, 165 167 N, species, two phases, aqueous systems, phasc equilibrium. 143 Null space, matrix equations, chemical equations as matrix equations, 93-95 Number of independent reactiona, aqueous systems. chemical equilibrium, 42-43

0 Oxidation-reduction reactions basic equations, 156- 158 Gibbs energy changes, 2

Index half-reactions hydrogen ion binding at specified pH, 167- 170 multiple spccics reactants at specified pH, 163- 165 methane monooxygenase reaction, 162- 163 nitrogenase reaction, 165- 167 research background, 155-156 single-species at specified pH, 158- 162 Oxygen hemoglobin tetramers, binding by, 122- 124 transformed Gibbs energy, specified concentration, 125 127

P Partial dissociation, tetramers into dimers, 127- 129 Pathway matrix, biochemical reactions linear equations, 107 matrix multiplication, net reactions, 106- 107 Phase equilibrium, aqueous systems carbon dioxide equilibrium, gas phase/aqueous solution distribution, 150G152 high polymers, 152- 153 molar properties of ions, electric potentials, 148- 149 research background, 141-142 two-phase systems chemical reaction, membrane permeability, single ion, 146- 147 transformed Gibbs energy, 148 chemical reaction and semipermeable membrane, 144 145 membrane permeability, single ion, 145 146 no chemical reaction, 142 -~ 143 Phase rule aqueous systems, chemical equilibrium, Gibbs-Duhem equation, 43-44 Gibbs-Duhem equation, 25-26 pH levels ATP binding of hydrogen and magnesium ions, 9- 11 biochemical reactions apparent equilibrium constants, 11 13 matrix equations, 95-97 biochemical thermodynamics, 2-3 apparent equilibrium constant, 63-65 fundamental equation, 58-62 Gibbs-Duhem equation, degrees of freedom, and equilibrium criterion, 70-71 Gibbs energy tansformations, apparent equilibrium constants, 74-76 hydrogen ion binding, 7 1-72 ionic strength, transformed properties tables, 76-86 magnesium ion binding, 72- 73 pseudoisomcr groups, 68- 69 reaction plots, 86-88 species/reactants, transformed properties, 65-66 temperature effects, 73-74 transformed properties, 66 --68 equilibrium constants, research background, 1-2 half-reactions at specified pH hydrogen ion binding, 167-170 multiple species reactants, 163-165 ionic strength and, 4-5 oxidation-reduction reactions -

395

basic equations, 157- 158 single species at specified pH, 158 162 oxygen binding, hemoglobin tetrarmers, 122- 124 protein-ligand equilibria, 134-138 semigrand ensemble partition function two pseudoisomer groups, 183 weak acid systems, 181-183 Phosphate compounds, glycolysis reactions, 115-1 17 Planck’s constants, thermodynamic potcntials, monatomic ideal gas, 33-34 pMg levels, adenosine triphosphate (ATP), hydrogen and magnesium ion production, 14-15 Proteins, hgand binding thermodynamics diprotic acid dissociation, 132- 133 equilibrium constants, determination, 129- 132 oxygen binding, hemoglobin tetramers, 122--124 pH levels, 134-138 research background, 121-122 tetramer-to-dimer partial dissociation, 127 129 transformed Gibbs energy fumarasc catalysis, 138-139 oxygen concentrations, 125-127 Pseudoisomers biochemical reactions at specified pH, 61-62 apparent equilibrium constant derivation, 63--65 species and reactants, transformed thermodynamic properties, 65-66 thermodynamic reactions. 68- 69 calorimetry, transformed entropy of biochemical reactions, 174-175 composition calculations, I 1 1-1 14 equilibrium calculations, biochemical reaction systems, 109.- 110 semigrand ensemble partition function coenzyme concentrations, 183- 184 two-system groups at specified pH, 183 weak acid systems as specific pH, 181 183 transformed Gibbs energy, specified oxygen concentration. 125- 127 Pyruvate dehydrogenase, biochemical reactions at specified PH apparent equilibrium constants, 82, 85 transformed Gibbs energies, 82, 84 ~

R Reactants biochemical equations as matrix equations, 97 biochemical reactions at specified pH half-reactions with multiple species at specified pH. 163-165 hydrogen ions, binding calculations, 71 72 Legendre transform calculations for water reactants, 107-108 transformed thermodynamic properties, 65-66 table of ionic strengths, 79-81 calorimetric measurements, transformed enthalpy of reaction from species formation, 173- 174 Reaction entropy, aqueous systems, chemical equilibrium, 41-43

396

Index

Reaction equations biochemical reactions, matrix equations, 95--97 chemical reactions, matrix equations, 90 95 Reaction Gibbs energy, aqueous systems, chemical equilibrium constant derivation, 36-38 Reaction volume, aqueous systems, chemical equilibrium, 41-43 Reciprocal effects, ATP binding of hydrogen and magnesium ions, 1 1 Reduction potentials nitrogenase reaction, 165 167 oxidation-reduction reactions, 156- 158 half-reactions with multiple species at specified pH, 163-165 single species at specified pH, 158- 162

S Sackur-Tetrode equation, thermodynamic potentials. monatomic ideal gas, 33-34 Second law of thermodynamics entropy and, 19 -20 internal energy equations, 21-24 Semigrand ensemble partition function biochemical reactions, coenzyme concentrations, 183 I84 future research issues, 184-185 pseudoisomer groups at specified pH, 183 research background, 179- 180 single species single-phase systems, thermodynamic potentials, 31 32 statistical mechanics, 179- 181 transformed Gibbs energy, weak acid systems at specified pH, 181-183 Semipermeable membrane. See also Membranc permeability aqueous systems, two-phase systems, chemical reaction, 144- 145 Single ion, membrane permeability with, two-phase aqueous systems chemical reaction, 146- 147 phase equilibrium. 145- 146 transformed Gibbs energy, 148 Single-phase systems. Legendre transforms for thermodynamic potentials, 27-30 Single species single-phase systcms. thermodynamic potentials, 30 ~ 3 2 Single species two-phase systems, aqueous systems, phase equilibrium, 142 - 143 Species formation, calorimetric measurements, transformed enthalpy of reaction from, 172- 174 Standard chemical potential, aqueous systems, chemical equilibrium constant derivation, 37- 38 Statistical mechanics, scmigrand ensemble partition function, 179- 18 1 Stoichionietric numbers biochemical reactions a t specified pH, apparent equilibrium constant derivation, 63 65 equilibrium calculations, biochemical reaction systems, 109- 110 ma trices biochemical coupling reactions, 9 7 ~99 biochemical equations a s matrix equations, 96- 97

chemical,/biochemica1 thermodynamics, 89-90 chemical equations as matrix equations, 91 - 95 glycolysis reactions, 115-1 17 water reactants, Legendre transform calculations. 107- 108 net biochemical reactions, matrix multiplication, 106- 107 Sums of species biochemical thermodynamics, 3 equilibrium constants, research background, 1 2 ~

T Tempcraturc effects aqueous systems, chemical equilibrium, thermodynamic properties, 47-49 biochemical reactions a t specified pH, transformed thermodynamic properties, 73-74 calorimetry of biochemical reactions, 176- 177 Tet ramen hemoglobin, oxygen binding by, 122- 124 partial dissociation into dimers, 127- 129 Thermodynamic potentials Legelidre transforms for, 26-30 monatomic ideal gas, derivatives, 32-34 properties of, 20 single-phase systems, one species, 3 0 ~32 Thermodynamics aqueous systems, chemical equilibrium, 38-43 biochemical species, thermodynamic tables, 49 55 isomer groups, 44-46 temperature effects, 47-49 biochemical reactions research background, 2-3 specified pH apparent equilibrium constant. 63--65 fundamental equation, 58- 62 Gibbs-Duhem equation, degrees of freedom. and equilibrium criterion, 70 71 Gibbs energy tansformations, apparent equilibrium constants, 74 - 76 hydrogen ion binding, 71-72 ionic strength, transformed properties tables, 76-86 magnesium ion binding, 72-73 pseudoisomer groups, 68- 69 rcaction plots, 86-88 species/reactants, transformed properties. 6 5 ~66 temperature effects, 73-74 transformed properties, 66-68 conjugate properties, 32 equilibrium constants, research background, 1 2 Gibbs-Duhem equation and phase rule. 25-26 intcrnal encrgy equation, 21 24 laws and principles, 19 20 Legendre transforms, additional potentials, 26 30 matrices, chemical and biochehical reactions biochemical matrix equations, 95-97 biochemical reaction coupling, 97 99 chemical matrix cquations, 90-95 chemical reaction systems, fundamental equations. 99-101 fundamental equations, biological rcaction systems. 101 102 linear algebra operations, 103 ~

~

-~

Index Maxwell equations, 24 -25 monatomic ideal gas properties, potential derivatives, 32-34 protein binding of ligands diprotic acid dissociation, 132-133 equilibrium constants, determination, 129-~132 oxygen binding, hemoglobin tetramers, 122 124 pH levels, 134-138 research background, 121-122 tetramer-to-dimer partial dissociation, 127-129 transformed Gibbs energy fuinarase catalysis, 138 139 oxygcn concentrations, 125- 127 single-phase system potentid, single species. 30-32 thermodynamic state, defined, 20-21 Thermodynamic state, properties of, 20-21 Transformation matrices chemical equations as matrix equations, 100- 101 lincar algebra, 103 Transformed Gibbs energy biochemical reactions at specified pH, 58-62 apparent equilibrium constant derivation, 64-65, 74-76 apparent equilibrium constants, tables, 76-86 composition calculations, 110-1 14 equilibrium conditions at glycolysis, 1 17- 119 thermodynamic properties, 66-68 water reactants, Legendre transform calculations, 107-108 caloriinetry, transformed entropy of biochemical reactions, 174-175 composition calculations, 113-114 fumarase catalysis, 13% 139 hemoglobin tetramers, oxygen binding by. 122-124 oxidation-reduction reactions ~

397

basic equations, 157 158 half-reactions and hydrogen ion binding, 169-170 methane monooxygenase reaction, 162- 163 single species at specified pH, 160-162 semigrand ensemble partition function and, weak acid systems at specified pH, 181- 183 tetramers, partial dissociation into dimers, 127-129 two-phase aqueous systems, chemical reaction and singleion membrane permeability, 148 Transformed thermodynamic properties, biochemical reactions at specified pH Gibbs energy of reaction, 66-68 ionic strength at 298.15 K, 76-86 species and reactants, 65-66 temperature effects, 73 -74 Two-phase aqueous systems, phase equilibrium chemical reaction, membrane permeability, single ion. 146 147 transformed Gibbs energy, 148 chemical reaction and semipermeable membrane, 144- 145 membrane permeability, single ion, 145 146 no chemical reaction, 142- 143 ~

W Water reactants, biochemical reactions, Lcgendre transform calculations, 107-108 Weak acids pK values, 15-17 semigrand ensemble partition function at specified pH, 181-1 83